Alignments for a candidate for glcB in Pseudomonas putida KT2440

GapMind for catabolism of small carbon sources

Alignments for a candidate for glcB in Pseudomonas putida KT2440

Align Malate synthase G (EC 2.3.3.9) (characterized)
to candidate PP_0356 PP_0356 malate synthase G

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



>FitnessBrowser__Putida:PP_0356
          Length = 725

 Score = 1215 bits (3144), Expect = 0.0
 Identities = 589/726 (81%), Positives = 664/726 (91%), Gaps = 1/726 (0%)

Query: 1   MTERVQVGGLQVAKVLYDFVNNEAIPGTGVDAAAFWAGADSVIHDLAPKNRALLAKRDDL 60
           MT  VQVGGLQVAKVLYDFVNNEAIPGTG+ A  FWAGA+ +I+DLAPKN+ALLAKRD+L
Sbjct: 1   MTGYVQVGGLQVAKVLYDFVNNEAIPGTGIVAEQFWAGAEKIINDLAPKNKALLAKRDEL 60

Query: 61  QAQIDAWHQARAGQAHDAVAYKSFLQEIGYLLPEAEDFQATTENVDEEIARMAGPQLVVP 120
           QA+IDAWHQAR GQAHDA AYK+FLQEIGYLLP+A+DFQATT+NVDEEIA MAGPQLVVP
Sbjct: 61  QAKIDAWHQARKGQAHDAAAYKAFLQEIGYLLPQADDFQATTQNVDEEIAHMAGPQLVVP 120

Query: 121 IMNARFALNAANARWGSLYDALYGTDAISEADGASKGPGYNEIRGNKVIAYARNFLNEAA 180
           +MNARFALNAANARWGSLYDALYGTDAIS+  GA KG GYN++RG+KVIA+AR FL+EAA
Sbjct: 121 VMNARFALNAANARWGSLYDALYGTDAISDEGGAEKGQGYNKVRGDKVIAFARAFLDEAA 180

Query: 181 PLETGSHVDSTGYRIEGGKLVVSLKDGSTTGLKNPAQLQGFQGEASAPIAVLLKNNGIHF 240
           PL  GSHVDSTGYRIEGGKLVV+LK GS TGL++ AQL GF G+A+AP AVLLK+NG+HF
Sbjct: 181 PLAAGSHVDSTGYRIEGGKLVVALKGGSNTGLRDDAQLIGFHGDAAAPTAVLLKHNGLHF 240

Query: 241 EIQIDPASPIGQTDAAGVKDILMESALTTIMDCEDSIAAVDADDKTVVYRNWLGLMKGDL 300
           EIQ+D ++P+G TDAAGVKDILMESALTTIMDCEDS+AAVDADDK +VYRNWLGLMKGDL
Sbjct: 241 EIQVDASTPVGSTDAAGVKDILMESALTTIMDCEDSVAAVDADDKVIVYRNWLGLMKGDL 300

Query: 301 VEELEKGGKRITRAMNPDRVYTKADGNGELTLHGRSLLFIRNVGHLMTNDAILDKEGNEV 360
            E + KGGK  TR MNPDR Y   +G G +TLHGRSLLF+RNVGHLMTN AILD +GNE+
Sbjct: 301 AESVSKGGKTFTRTMNPDREYAAPNG-GSVTLHGRSLLFVRNVGHLMTNPAILDAQGNEI 359

Query: 361 PEGIMDGLFTSLIAVHNLNGNTSRKNTRTGSMYIVKPKMHGPEEVAFATELFGRVEDVLG 420
           PEGI DGLFT+LIA+HNLNGNTSRKNTR+GS+YIVKPKMHGPEEVAFATE+F +VED+LG
Sbjct: 360 PEGIQDGLFTNLIALHNLNGNTSRKNTRSGSVYIVKPKMHGPEEVAFATEIFSQVEDLLG 419

Query: 421 LPRNTLKVGIMDEERRTTINLKACIKEARERVVFINTGFLDRTGDEIHTSMEAGPMVRKA 480
           +PRNT+KVGIMDEERRTT+NLK+CIK A ERVVFINTGFLDRTGDEIHTSMEAG +VRK 
Sbjct: 420 MPRNTVKVGIMDEERRTTVNLKSCIKAAAERVVFINTGFLDRTGDEIHTSMEAGAVVRKG 479

Query: 481 AMKAEKWISAYENNNVDVGLACGLQGKAQIGKGMWAMPDLMAAMLEQKVGHPMAGANTAW 540
           AMK EKWI AYENNNVDVGLA GLQG+AQIGKGMWAMPDLMAAMLEQK+ HP+AGANTAW
Sbjct: 480 AMKNEKWIGAYENNNVDVGLATGLQGRAQIGKGMWAMPDLMAAMLEQKIAHPLAGANTAW 539

Query: 541 VPSPTAATLHAMHYHKIDVQARQVELAKREKASIDDILTIPLAQDTNWSEEEKRNELDNN 600
           VPSPTAATLHA+HYHK+DVQARQ ELA R  AS+DDIL IPLA DTNWS EE RNELDNN
Sbjct: 540 VPSPTAATLHALHYHKVDVQARQRELASRTPASVDDILAIPLAADTNWSAEEIRNELDNN 599

Query: 601 SQGILGYMVRWVEQGVGCSKVPDINDIALMEDRATLRISSQHVANWMRHGVVTKDQVVES 660
           +QGILGY+VRW++QGVGCSKVPDIN++ LMEDRATLRIS+Q +ANW+RHGVV+++QV+ES
Sbjct: 600 AQGILGYVVRWIDQGVGCSKVPDINNVGLMEDRATLRISAQLLANWLRHGVVSQEQVLES 659

Query: 661 LKRMAPVVDRQNQGDPLYRPMAPDFDNSVAFQAALELVLEGTKQPNGYTEPVLHRRRREF 720
           LKRMA VVD+QN GDPLYRPMAP+FD++VAFQAA+ELV+EG KQPNGYTEPVLHRRRREF
Sbjct: 660 LKRMAVVVDQQNAGDPLYRPMAPNFDDNVAFQAAVELVVEGGKQPNGYTEPVLHRRRREF 719

Query: 721 KAKNGL 726
           KA+NGL
Sbjct: 720 KARNGL 725


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: 1614
Number of extensions: 52
Number of successful extensions: 2
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: 725
Length adjustment: 40
Effective length of query: 686
Effective length of database: 685
Effective search space:   469910
Effective search space used:   469910
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 PP_0356 PP_0356 (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.21249.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 1207.6   1.5          0 1207.4   1.5    1.0  1  lcl|FitnessBrowser__Putida:PP_0356  PP_0356 malate synthase G


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Putida:PP_0356  PP_0356 malate synthase G
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1207.4   1.5         0         0       2     720 ..       4     722 ..       3     723 .. 0.99

  Alignments for each domain:
  == domain 1  score: 1207.4 bits;  conditional E-value: 0
                           TIGR01345   2 rvdagrlqvakklkdfveeevlpgtgvdaekfwsgfdeivrdlapenrellakrdeiqaaideyhrknk.gvidk 75 
                                         +v++g+lqvak+l+dfv++e++pgtg+ ae+fw+g ++i++dlap+n+ llakrde+qa id++h+  k  + d 
  lcl|FitnessBrowser__Putida:PP_0356   4 YVQVGGLQVAKVLYDFVNNEAIPGTGIVAEQFWAGAEKIINDLAPKNKALLAKRDELQAKIDAWHQARKgQAHDA 78 
                                         6899****************************************************************955789* PP

                           TIGR01345  76 eayksflkeigylveepervtietenvdseiasqagpqlvvpvlnaryalnaanarwgslydalygsnvipeedg 150
                                         +ayk fl+eigyl ++ +  + +t+nvd+eia  agpqlvvpv+nar+alnaanarwgslydalyg+++i++e+g
  lcl|FitnessBrowser__Putida:PP_0356  79 AAYKAFLQEIGYLLPQADDFQATTQNVDEEIAHMAGPQLVVPVMNARFALNAANARWGSLYDALYGTDAISDEGG 153
                                         *************************************************************************** PP

                           TIGR01345 151 aekgkeynpkrgekviefarefldeslplesgsyadvvkykivdkklavqlesgkvtrlkdeeqfvgyrgdaadp 225
                                         aekg+ yn +rg+kvi+far flde+ pl +gs+ d   y+i  +kl+v l+ g+ t l+d++q +g++gdaa+p
  lcl|FitnessBrowser__Putida:PP_0356 154 AEKGQGYNKVRGDKVIAFARAFLDEAAPLAAGSHVDSTGYRIEGGKLVVALKGGSNTGLRDDAQLIGFHGDAAAP 228
                                         *************************************************************************** PP

                           TIGR01345 226 evillktnglhielqidarhpigkadkakvkdivlesaittildcedsvaavdaedkvlvyrnllglmkgtlkek 300
                                         +++llk+nglh e+q+da  p+g +d a+vkdi++esa+tti+dcedsvaavda+dkv+vyrn+lglmkg+l e 
  lcl|FitnessBrowser__Putida:PP_0356 229 TAVLLKHNGLHFEIQVDASTPVGSTDAAGVKDILMESALTTIMDCEDSVAAVDADDKVIVYRNWLGLMKGDLAES 303
                                         *************************************************************************** PP

                           TIGR01345 301 lekngriikrklnedrsytaangeelslhgrsllfvrnvghlmtipviltdegeeipegildgvltsvialydlk 375
                                         ++k g++++r +n dr+y a+ng  ++lhgrsllfvrnvghlmt+p+il+ +g+eipegi dg++t++ial++l+
  lcl|FitnessBrowser__Putida:PP_0356 304 VSKGGKTFTRTMNPDREYAAPNGGSVTLHGRSLLFVRNVGHLMTNPAILDAQGNEIPEGIQDGLFTNLIALHNLN 378
                                         *************************************************************************** PP

                           TIGR01345 376 vqnklrnsrkgsvyivkpkmhgpeevafanklftriedllglerhtlkvgvmdeerrtslnlkaciakvkervaf 450
                                          + + +n+r gsvyivkpkmhgpeevafa ++f+++edllg++r+t+kvg+mdeerrt++nlk+ci+ ++erv+f
  lcl|FitnessBrowser__Putida:PP_0356 379 GNTSRKNTRSGSVYIVKPKMHGPEEVAFATEIFSQVEDLLGMPRNTVKVGIMDEERRTTVNLKSCIKAAAERVVF 453
                                         *************************************************************************** PP

                           TIGR01345 451 intgfldrtgdeihtsmeagamvrkadmksapwlkayernnvaagltcglrgkaqigkgmwampdlmaemlekkg 525
                                         intgfldrtgdeihtsmeaga+vrk+ mk   w+ aye+nnv+ gl +gl+g+aqigkgmwampdlma mle+k+
  lcl|FitnessBrowser__Putida:PP_0356 454 INTGFLDRTGDEIHTSMEAGAVVRKGAMKNEKWIGAYENNNVDVGLATGLQGRAQIGKGMWAMPDLMAAMLEQKI 528
                                         *************************************************************************** PP

                           TIGR01345 526 dqlragantawvpsptaatlhalhyhrvdvqkvqkeladaerraelkeiltipvaentnwseeeikeeldnnvqg 600
                                           + agantawvpsptaatlhalhyh+vdvq+ q ela+  + a+ ++il ip+a +tnws+eei++eldnn+qg
  lcl|FitnessBrowser__Putida:PP_0356 529 AHPLAGANTAWVPSPTAATLHALHYHKVDVQARQRELASR-TPASVDDILAIPLAADTNWSAEEIRNELDNNAQG 602
                                         **************************************98.8999****************************** PP

                           TIGR01345 601 ilgyvvrwveqgigcskvpdihnvalmedratlrissqhlanwlrhgivskeqvleslermakvvdkqnagdeay 675
                                         ilgyvvrw++qg+gcskvpdi nv lmedratlris+q lanwlrhg+vs+eqvlesl+rma+vvd+qnagd+ y
  lcl|FitnessBrowser__Putida:PP_0356 603 ILGYVVRWIDQGVGCSKVPDINNVGLMEDRATLRISAQLLANWLRHGVVSQEQVLESLKRMAVVVDQQNAGDPLY 677
                                         *************************************************************************** PP

                           TIGR01345 676 rpmadnleasvafkaakdlilkgtkqpsgytepilharrlefkek 720
                                         rpma+n+++ vaf+aa +l+++g kqp+gytep+lh+rr+efk++
  lcl|FitnessBrowser__Putida:PP_0356 678 RPMAPNFDDNVAFQAAVELVVEGGKQPNGYTEPVLHRRRREFKAR 722
                                         *******************************************87 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (721 nodes)
Target sequences:                          1  (725 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: 0.05u 0.03s 00:00:00.08 Elapsed: 00:00:00.07
# Mc/sec: 7.09
//
[ok]

This GapMind analysis is from Sep 17 2021. 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 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