Alignments for a candidate for glcB in Polaromonas naphthalenivorans CJ2

GapMind for catabolism of small carbon sources

Alignments for a candidate for glcB in Polaromonas naphthalenivorans CJ2

Align Malate synthase G (EC 2.3.3.9) (characterized)
to candidate WP_011803045.1 PNAP_RS18410 malate synthase G

Query= reanno::psRCH2:GFF353
         (726 letters)



>NCBI__GCF_000015505.1:WP_011803045.1
          Length = 730

 Score =  965 bits (2494), Expect = 0.0
 Identities = 473/729 (64%), Positives = 585/729 (80%), Gaps = 9/729 (1%)

Query: 1   MTERVQVGGLQVAKVLYDFVNNEAIPGTGVDAAAFWAGADSVIHDLAPKNRALLAKRDDL 60
           MTER     LQVA  LY F+ ++ +PGTGVD+  FW+G D+++ DLAPKN ALLA+RD L
Sbjct: 1   MTERTTRHSLQVATELYRFIEDKVLPGTGVDSDKFWSGFDAIVADLAPKNIALLAERDRL 60

Query: 61  QAQIDAWHQARAGQAHDAVAYKSFLQEIGYLLPEAEDFQATTENVDEEIARMAGPQLVVP 120
           Q ++DAWH+A  G   D  AY++FL+ IGYL+P+ E    TT NVD E+A  AGPQLVVP
Sbjct: 61  QLEMDAWHKANPGPIADMPAYRAFLESIGYLVPQPETVAVTTANVDAELAVQAGPQLVVP 120

Query: 121 IMNARFALNAANARWGSLYDALYGTDAISEADGASKGPGYNEIRGNKVIAYARNFLNEAA 180
           ++NAR+ALNAANARWGSLYDALYGTDAI E DGA KG GYN +RG KVIA+ARN L++AA
Sbjct: 121 VLNARYALNAANARWGSLYDALYGTDAIPETDGAEKGKGYNPVRGAKVIAFARNLLDQAA 180

Query: 181 PLETGSHVDSTGYRIEGGKLVVSLKDGSTTGLKNPAQLQGFQGEASAPIAVLLKNNGIHF 240
           PL TGSH D+TGY IEGG+LVV+   G + GL++PAQL G++G+A+AP +VLL +NG+H 
Sbjct: 181 PLSTGSHKDATGYSIEGGQLVVTQASGMS-GLQDPAQLVGYRGDAAAPSSVLLVHNGLHI 239

Query: 241 EIQIDPASPIGQTDAAGVKDILMESALTTIMDCEDSIAAVDADDKTVVYRNWLGLMKGDL 300
           +I ID A+ +G++DAAG+ D+++ESAL+TI+D EDS+A VDA+DK + Y NWLG+++G L
Sbjct: 240 DIIIDRATTLGKSDAAGISDMVIESALSTILDLEDSVAVVDAEDKVLAYGNWLGILQGTL 299

Query: 301 VEELEKGGKRITRAMNPDRVYTKADGNGELTLHGRSLLFIRNVGHLMTNDAILDKEGNEV 360
            EE+ KGG   TR +NPDRVYT ADG GE+TLHGRSL+F+RNVGHLMTN AIL   G E+
Sbjct: 300 TEEVSKGGTTFTRGLNPDRVYTAADG-GEVTLHGRSLMFVRNVGHLMTNPAILYAGGKEI 358

Query: 361 PEGIMDGLFTSLIAVHNLN--GNTSRKNTRTGSMYIVKPKMHGPEEVAFATELFGRVEDV 418
           PEGIMD + T+ IA+H+    G    KN+RTGS+YIVKPKMHGP EVAFA ELFGRVE +
Sbjct: 359 PEGIMDAVVTTTIAIHDFKRQGQPGIKNSRTGSVYIVKPKMHGPAEVAFAAELFGRVEAL 418

Query: 419 LGLPRNTLKVGIMDEERRTTINLKACIKEARERVVFINTGFLDRTGDEIHTSMEAGPMVR 478
           LGLP NT+K+GIMDEERRT++NLKACI EA  RV FINTGFLDRTGDE+HT+M+AGPM+R
Sbjct: 419 LGLPANTVKLGIMDEERRTSVNLKACIAEAEARVAFINTGFLDRTGDEMHTAMQAGPMIR 478

Query: 479 KAAMKAEKWISAYENNNVDVGLACGLQGKAQIGKGMWAMPDLMAAMLEQKVGHPMAGANT 538
           K  MK   WI+AYE NNV VGL+CGL+GKAQIGKGMWAMPDLMAAMLEQK+GHP AGANT
Sbjct: 479 KGDMKTSAWIAAYEKNNVLVGLSCGLRGKAQIGKGMWAMPDLMAAMLEQKIGHPKAGANT 538

Query: 539 AWVPSPTAATLHAMHYHKIDVQARQVELAKREKAS-----IDDILTIPLAQDTNWSEEEK 593
           AWVPSPTAATLHA+HYH++ V   Q EL K +  +     ++ +L IP+    NWS+ EK
Sbjct: 539 AWVPSPTAATLHALHYHQVLVSDVQKELEKIDANAERGNLLNGLLQIPVTATPNWSDAEK 598

Query: 594 RNELDNNSQGILGYMVRWVEQGVGCSKVPDINDIALMEDRATLRISSQHVANWMRHGVVT 653
           + ELDNN+QGILGY+VRW++QGVGCSKVPDI++IALMEDRATLRISSQH+ANW+ HGVVT
Sbjct: 599 QQELDNNAQGILGYVVRWIDQGVGCSKVPDIHNIALMEDRATLRISSQHMANWLHHGVVT 658

Query: 654 KDQVVESLKRMAPVVDRQNQGDPLYRPMAPDFDNSVAFQAALELVLEGTKQPNGYTEPVL 713
           + QV E+ +RMA VVD QN GDPLY+ MA  FD S A++AA +LV +G +QP+GYTEP+L
Sbjct: 659 EAQVKETFERMAAVVDGQNAGDPLYKNMAGHFDTSAAYKAACDLVFKGLEQPSGYTEPLL 718

Query: 714 HRRRREFKA 722
           H  R + KA
Sbjct: 719 HAWRLKVKA 727


Lambda     K      H
   0.316    0.133    0.386 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 1477
Number of extensions: 59
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 726
Length of database: 730
Length adjustment: 40
Effective length of query: 686
Effective length of database: 690
Effective search space:   473340
Effective search space used:   473340
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 55 (25.8 bits)

Align candidate WP_011803045.1 PNAP_RS18410 (malate synthase G)
to HMM TIGR01345 (glcB: malate synthase G (EC 2.3.3.9))

# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file:                  ../tmp/path.carbon/TIGR01345.hmm
# target sequence database:        /tmp/gapView.3248991.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01345  [M=721]
Accession:   TIGR01345
Description: malate_syn_G: malate synthase G
Scores for complete sequences (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Sequence                             Description
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
          0 1204.8   0.0          0 1204.6   0.0    1.0  1  NCBI__GCF_000015505.1:WP_011803045.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000015505.1:WP_011803045.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1204.6   0.0         0         0       3     719 ..       5     727 ..       3     729 .. 0.98

  Alignments for each domain:
  == domain 1  score: 1204.6 bits;  conditional E-value: 0
                             TIGR01345   3 vdagrlqvakklkdfveeevlpgtgvdaekfwsgfdeivrdlapenrellakrdeiqaaideyhrknk.gvid 74 
                                            +  +lqva++l++f+e++vlpgtgvd++kfwsgfd+iv dlap+n  lla+rd++q  +d++h+ n+ +  d
  NCBI__GCF_000015505.1:WP_011803045.1   5 TTRHSLQVATELYRFIEDKVLPGTGVDSDKFWSGFDAIVADLAPKNIALLAERDRLQLEMDAWHKANPgPIAD 77 
                                           56789***************************************************************55569 PP

                             TIGR01345  75 keayksflkeigylveepervtietenvdseiasqagpqlvvpvlnaryalnaanarwgslydalygsnvipe 147
                                             ay+ fl+ igylv++pe+v ++t nvd+e+a qagpqlvvpvlnaryalnaanarwgslydalyg+++ipe
  NCBI__GCF_000015505.1:WP_011803045.1  78 MPAYRAFLESIGYLVPQPETVAVTTANVDAELAVQAGPQLVVPVLNARYALNAANARWGSLYDALYGTDAIPE 150
                                           9************************************************************************ PP

                             TIGR01345 148 edgaekgkeynpkrgekviefarefldeslplesgsyadvvkykivdkklavqlesgkvtrlkdeeqfvgyrg 220
                                           +dgaekgk ynp+rg kvi+far++ld++ pl++gs++d+  y+i  ++l+v+     +  l+d++q vgyrg
  NCBI__GCF_000015505.1:WP_011803045.1 151 TDGAEKGKGYNPVRGAKVIAFARNLLDQAAPLSTGSHKDATGYSIEGGQLVVTQA-SGMSGLQDPAQLVGYRG 222
                                           ****************************************************988.56899************ PP

                             TIGR01345 221 daadpevillktnglhielqidarhpigkadkakvkdivlesaittildcedsvaavdaedkvlvyrnllglm 293
                                           daa+p+ +ll +nglhi++ id    +gk+d a++ d+v+esa++tild+edsva vdaedkvl y n+lg+ 
  NCBI__GCF_000015505.1:WP_011803045.1 223 DAAAPSSVLLVHNGLHIDIIIDRATTLGKSDAAGISDMVIESALSTILDLEDSVAVVDAEDKVLAYGNWLGIL 295
                                           ************************************************************************* PP

                             TIGR01345 294 kgtlkeklekngriikrklnedrsytaangeelslhgrsllfvrnvghlmtipviltdegeeipegildgvlt 366
                                           +gtl e+++k g +++r ln dr+ytaa+g e++lhgrsl+fvrnvghlmt+p+il   g+eipegi+d+v+t
  NCBI__GCF_000015505.1:WP_011803045.1 296 QGTLTEEVSKGGTTFTRGLNPDRVYTAADGGEVTLHGRSLMFVRNVGHLMTNPAILYAGGKEIPEGIMDAVVT 368
                                           ************************************************************************* PP

                             TIGR01345 367 svialydlkvqnk..lrnsrkgsvyivkpkmhgpeevafanklftriedllglerhtlkvgvmdeerrtslnl 437
                                           + ia++d+k+q++  ++nsr+gsvyivkpkmhgp evafa +lf+r+e llgl+ +t+k+g+mdeerrts+nl
  NCBI__GCF_000015505.1:WP_011803045.1 369 TTIAIHDFKRQGQpgIKNSRTGSVYIVKPKMHGPAEVAFAAELFGRVEALLGLPANTVKLGIMDEERRTSVNL 441
                                           *********9875559********************************************************* PP

                             TIGR01345 438 kaciakvkervafintgfldrtgdeihtsmeagamvrkadmksapwlkayernnvaagltcglrgkaqigkgm 510
                                           kacia+++ rvafintgfldrtgde+ht+m+ag+m+rk+dmk+++w+ aye+nnv+ gl cglrgkaqigkgm
  NCBI__GCF_000015505.1:WP_011803045.1 442 KACIAEAEARVAFINTGFLDRTGDEMHTAMQAGPMIRKGDMKTSAWIAAYEKNNVLVGLSCGLRGKAQIGKGM 514
                                           ************************************************************************* PP

                             TIGR01345 511 wampdlmaemlekkgdqlragantawvpsptaatlhalhyhrvdvqkvqkeladaerrae....lkeiltipv 579
                                           wampdlma mle+k++ ++agantawvpsptaatlhalhyh+v v  vqkel + + +ae    l+ +l+ipv
  NCBI__GCF_000015505.1:WP_011803045.1 515 WAMPDLMAAMLEQKIGHPKAGANTAWVPSPTAATLHALHYHQVLVSDVQKELEKIDANAErgnlLNGLLQIPV 587
                                           ****************************************************999999885666777899*** PP

                             TIGR01345 580 aentnwseeeikeeldnnvqgilgyvvrwveqgigcskvpdihnvalmedratlrissqhlanwlrhgivske 652
                                           + + nws+ e+++eldnn+qgilgyvvrw++qg+gcskvpdihn+almedratlrissqh+anwl hg+v+  
  NCBI__GCF_000015505.1:WP_011803045.1 588 TATPNWSDAEKQQELDNNAQGILGYVVRWIDQGVGCSKVPDIHNIALMEDRATLRISSQHMANWLHHGVVTEA 660
                                           ************************************************************************* PP

                             TIGR01345 653 qvleslermakvvdkqnagdeayrpmadnleasvafkaakdlilkgtkqpsgytepilharrlefke 719
                                           qv e++erma vvd qnagd+ y++ma+ +++s a+kaa dl++kg +qpsgytep+lha+rl+ k+
  NCBI__GCF_000015505.1:WP_011803045.1 661 QVKETFERMAAVVDGQNAGDPLYKNMAGHFDTSAAYKAACDLVFKGLEQPSGYTEPLLHAWRLKVKA 727
                                           ****************************************************************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (721 nodes)
Target sequences:                          1  (730 residues searched)
Passed MSV filter:                         1  (1); expected 0.0 (0.02)
Passed bias filter:                        1  (1); expected 0.0 (0.02)
Passed Vit filter:                         1  (1); expected 0.0 (0.001)
Passed Fwd filter:                         1  (1); expected 0.0 (1e-05)
Initial search space (Z):                  1  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 39.29
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

the paper from 2019 on GapMind for amino acid biosynthesis
the 2024 update on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory

GapMind for catabolism of small carbon sources