GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glcB in Desulfovibrio vulgaris Miyazaki F

Align Malate synthase G (EC 2.3.3.9) (characterized)
to candidate 8501453 DvMF_2183 malate synthase G (RefSeq)

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



>FitnessBrowser__Miya:8501453
          Length = 731

 Score =  930 bits (2404), Expect = 0.0
 Identities = 460/731 (62%), Positives = 558/731 (76%), Gaps = 6/731 (0%)

Query: 1   MTERVQVGGLQVAKVLYDFVNNEAIPGTGVDAAAFWAGADSVIHDLAPKNRALLAKRDDL 60
           MT+RVQVGGLQ+A  LYD +  +  PGTGVD   FW   ++++  +A +NRALLAKR +L
Sbjct: 1   MTQRVQVGGLQIAAPLYDVIVRDIAPGTGVDPDRFWTALENMVETMADRNRALLAKRAEL 60

Query: 61  QAQIDAWHQARAGQAHDAVAYKSFLQEIGYLLPEAEDFQATTENVDEEIARMAGPQLVVP 120
           Q  IDAWH+ R G  HD  AY++FL+ IGYL+PE  DF  TTE VD EIA +AGPQLVVP
Sbjct: 61  QDAIDAWHRERRGTPHDGAAYEAFLRSIGYLVPEGPDFAVTTEGVDPEIALVAGPQLVVP 120

Query: 121 IMNARFALNAANARWGSLYDALYGTDAISE---ADGASKGPGYNEIRGNKVIAYARNFLN 177
           I NAR+ALNAANARWGSLYDALYGTD I E     GA +G  YN  RG  V+A A  FL+
Sbjct: 121 ITNARYALNAANARWGSLYDALYGTDVIPEDPARGGAPRGGAYNPARGALVVARAAAFLD 180

Query: 178 EAAPLETGSHVDSTGYRIEGGKLVVSLKDGSTTGLKNPAQLQGFQGE-ASAPIAVLLKNN 236
           EA PL TGSH D+  Y + GGKL V LKDG+ TGL +PA+  G  G+ A    AVLL+N+
Sbjct: 181 EAFPLATGSHADAARYDVRGGKLAVILKDGAETGLADPARFVGHAGDPAGGNGAVLLRNH 240

Query: 237 GIHFEIQIDPASPIGQTDAAGVKDILMESALTTIMDCEDSIAAVDADDKTVVYRNWLGLM 296
           G+H EI+ID    IG+  AAGV+D++ME+A+TTI+DCEDS+A VD  DK + YRN LGL 
Sbjct: 241 GLHAEIRIDREHAIGRGHAAGVRDVVMEAAMTTILDCEDSVAVVDGADKALAYRNMLGLF 300

Query: 297 KGDLVEELEKGGKRITRAMNPDRVYTKADGNGELTLHGRSLLFIRNVGHLMTNDAILDKE 356
           +GDL  E  KGG+ + R +NPDR YT  DG    +L GRSLL +R VGHLMT DA+L + 
Sbjct: 301 RGDLSAEFPKGGRSVLRTLNPDREYTGPDG-AAFSLPGRSLLLVRTVGHLMTTDAVLARS 359

Query: 357 GNEVPEGIMDGLFTSLIAVHNLNGNTSRKNTRTGSMYIVKPKMHGPEEVAFATELFGRVE 416
           G E+PEG++D + T+ IA+H+L G +S +N+RTG +YIVKPK HGPEEVAF  ELF   E
Sbjct: 360 GEEIPEGMLDTMATAYIALHDLRGTSSVRNSRTGGVYIVKPKQHGPEEVAFTVELFRMAE 419

Query: 417 DVLGLPRNTLKVGIMDEERRTTINLKACIKEARERVVFINTGFLDRTGDEIHTSMEAGPM 476
           D LG+PRNTLK+GIMDEERRTT+NLK CI+ A ERV+FINTGFLDRTGDEIHT MEAGP+
Sbjct: 420 DALGMPRNTLKIGIMDEERRTTVNLKECIRAAAERVIFINTGFLDRTGDEIHTCMEAGPV 479

Query: 477 VRKAAMKAEKWISAYENNNVDVGLACGLQGKAQIGKGMWAMPDLMAAMLEQKVGHPMAGA 536
           VRK AM+ E+WI AYE+ NVD GLACGL G+AQ+GKGMWA PD+M  M+E K+GHP AGA
Sbjct: 480 VRKNAMRGERWIIAYEDWNVDTGLACGLAGRAQVGKGMWAKPDMMREMVETKIGHPRAGA 539

Query: 537 NTAWVPSPTAATLHAMHYHKIDVQARQVELAKREKASIDDILTIPL-AQDTNWSEEEKRN 595
           N AWVPSPTAATLHAMHYH +DV A Q  LA + +A++ D+LT+PL    +  + +E   
Sbjct: 540 NCAWVPSPTAATLHAMHYHAVDVAAVQKTLAGQRRATLADLLTLPLMGPASRPTPQEVEE 599

Query: 596 ELDNNSQGILGYMVRWVEQGVGCSKVPDINDIALMEDRATLRISSQHVANWMRHGVVTKD 655
           EL NN+Q ILGY+VRWVEQG+GCSKVPDI D+ LMEDRATLRISSQH+ANW+ HG+ T+D
Sbjct: 600 ELANNAQSILGYVVRWVEQGIGCSKVPDITDVGLMEDRATLRISSQHIANWLHHGICTRD 659

Query: 656 QVVESLKRMAPVVDRQNQGDPLYRPMAPDFDNSVAFQAALELVLEGTKQPNGYTEPVLHR 715
           QVV  LKRMA VVDRQN GDP YRPM+ DFD SVAFQAA +LVL G +QP+GYTEP+LH 
Sbjct: 660 QVVAVLKRMAAVVDRQNAGDPAYRPMSADFDASVAFQAACDLVLLGREQPSGYTEPILHA 719

Query: 716 RRREFKAKNGL 726
           RR+E KAK G+
Sbjct: 720 RRQEAKAKFGI 730


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: 1424
Number of extensions: 47
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: 731
Length adjustment: 40
Effective length of query: 686
Effective length of database: 691
Effective search space:   474026
Effective search space used:   474026
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 8501453 DvMF_2183 (malate synthase G (RefSeq))
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.12047.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 1070.9   0.0          0 1070.7   0.0    1.0  1  lcl|FitnessBrowser__Miya:8501453  DvMF_2183 malate synthase G (Ref


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Miya:8501453  DvMF_2183 malate synthase G (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1070.7   0.0         0         0       1     720 [.       3     727 ..       3     728 .. 0.98

  Alignments for each domain:
  == domain 1  score: 1070.7 bits;  conditional E-value: 0
                         TIGR01345   1 ervdagrlqvakklkdfveeevlpgtgvdaekfwsgfdeivrdlapenrellakrdeiqaaideyhrknk.gvidke 76 
                                       +rv++g+lq+a+ l+d + +++ pgtgvd + fw++++++v+ +a +nr llakr e+q aid++hr+ + ++ d +
  lcl|FitnessBrowser__Miya:8501453   3 QRVQVGGLQIAAPLYDVIVRDIAPGTGVDPDRFWTALENMVETMADRNRALLAKRAELQDAIDAWHRERRgTPHDGA 79 
                                       5799****************************************************************995679*** PP

                         TIGR01345  77 ayksflkeigylveepervtietenvdseiasqagpqlvvpvlnaryalnaanarwgslydalygsnvipee...dg 150
                                       ay+ fl+ igylv+e     ++te+vd eia  agpqlvvp++naryalnaanarwgslydalyg++vipe+   +g
  lcl|FitnessBrowser__Miya:8501453  80 AYEAFLRSIGYLVPEGPDFAVTTEGVDPEIALVAGPQLVVPITNARYALNAANARWGSLYDALYGTDVIPEDparGG 156
                                       *********************************************************************99644478 PP

                         TIGR01345 151 aekgkeynpkrgekviefarefldeslplesgsyadvvkykivdkklavqlesgkvtrlkdeeqfvgyrgdaa.dpe 226
                                       a +g+ ynp rg  v++ a  flde++pl +gs+ad+ +y++  +klav l++g +t l d+++fvg+ gd a    
  lcl|FitnessBrowser__Miya:8501453 157 APRGGAYNPARGALVVARAAAFLDEAFPLATGSHADAARYDVRGGKLAVILKDGAETGLADPARFVGHAGDPAgGNG 233
                                       99********************************************************************9761567 PP

                         TIGR01345 227 villktnglhielqidarhpigkadkakvkdivlesaittildcedsvaavdaedkvlvyrnllglmkgtlkeklek 303
                                       ++ll+++glh e++id +h ig+   a+v+d+v+e+a+ttildcedsva vd  dk l yrn+lgl +g+l +++ k
  lcl|FitnessBrowser__Miya:8501453 234 AVLLRNHGLHAEIRIDREHAIGRGHAAGVRDVVMEAAMTTILDCEDSVAVVDGADKALAYRNMLGLFRGDLSAEFPK 310
                                       9**************************************************************************** PP

                         TIGR01345 304 ngriikrklnedrsytaangeelslhgrsllfvrnvghlmtipviltdegeeipegildgvltsvialydlkvqnkl 380
                                        gr + r ln dr+yt+++g  +sl+grsll+vr vghlmt+ ++l  +geeipeg+ld++ t+ ial+dl+  +++
  lcl|FitnessBrowser__Miya:8501453 311 GGRSVLRTLNPDREYTGPDGAAFSLPGRSLLLVRTVGHLMTTDAVLARSGEEIPEGMLDTMATAYIALHDLRGTSSV 387
                                       ***************************************************************************** PP

                         TIGR01345 381 rnsrkgsvyivkpkmhgpeevafanklftriedllglerhtlkvgvmdeerrtslnlkaciakvkervafintgfld 457
                                       rnsr+g vyivkpk+hgpeevaf+ +lf   ed lg++r+tlk+g+mdeerrt++nlk ci  ++erv+fintgfld
  lcl|FitnessBrowser__Miya:8501453 388 RNSRTGGVYIVKPKQHGPEEVAFTVELFRMAEDALGMPRNTLKIGIMDEERRTTVNLKECIRAAAERVIFINTGFLD 464
                                       ***************************************************************************** PP

                         TIGR01345 458 rtgdeihtsmeagamvrkadmksapwlkayernnvaagltcglrgkaqigkgmwampdlmaemlekkgdqlragant 534
                                       rtgdeiht+meag++vrk+ m+   w+ aye  nv++gl cgl g+aq+gkgmwa pd+m em+e k++ +ragan 
  lcl|FitnessBrowser__Miya:8501453 465 RTGDEIHTCMEAGPVVRKNAMRGERWIIAYEDWNVDTGLACGLAGRAQVGKGMWAKPDMMREMVETKIGHPRAGANC 541
                                       ***************************************************************************** PP

                         TIGR01345 535 awvpsptaatlhalhyhrvdvqkvqkeladaerraelkeiltipvaent.nwseeeikeeldnnvqgilgyvvrwve 610
                                       awvpsptaatlha+hyh vdv +vqk+la + rra+l ++lt+p+ + +   + +e++eel nn+q+ilgyvvrwve
  lcl|FitnessBrowser__Miya:8501453 542 AWVPSPTAATLHAMHYHAVDVAAVQKTLAGQ-RRATLADLLTLPLMGPAsRPTPQEVEEELANNAQSILGYVVRWVE 617
                                       *****************************98.99**********9865516799*********************** PP

                         TIGR01345 611 qgigcskvpdihnvalmedratlrissqhlanwlrhgivskeqvleslermakvvdkqnagdeayrpmadnleasva 687
                                       qgigcskvpdi +v lmedratlrissqh+anwl hgi +++qv++ l+rma vvd+qnagd+ayrpm+ +++asva
  lcl|FitnessBrowser__Miya:8501453 618 QGIGCSKVPDITDVGLMEDRATLRISSQHIANWLHHGICTRDQVVAVLKRMAAVVDRQNAGDPAYRPMSADFDASVA 694
                                       ***************************************************************************** PP

                         TIGR01345 688 fkaakdlilkgtkqpsgytepilharrlefkek 720
                                       f+aa dl+l g +qpsgytepilharr+e k+k
  lcl|FitnessBrowser__Miya:8501453 695 FQAACDLVLLGREQPSGYTEPILHARRQEAKAK 727
                                       ******************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (721 nodes)
Target sequences:                          1  (731 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 0.02s 00:00:00.07 Elapsed: 00:00:00.06
# Mc/sec: 8.19
//
[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:

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:

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:

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:

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