Alignments for a candidate for garD in Herbaspirillum seropedicae SmR1

GapMind for catabolism of small carbon sources

Alignments for a candidate for garD in Herbaspirillum seropedicae SmR1

Align Galactarate dehydratase (EC 4.2.1.42) (characterized)
to candidate HSERO_RS15800 HSERO_RS15800 D-galactarate dehydratase

Query= reanno::HerbieS:HSERO_RS15800
         (522 letters)



>FitnessBrowser__HerbieS:HSERO_RS15800
          Length = 522

 Score = 1044 bits (2699), Expect = 0.0
 Identities = 522/522 (100%), Positives = 522/522 (100%)

Query: 1   MSTDTSASQASAPRYIMMNDTDNVAIVVNDGGLPAGTVFPDGLTLVDRVPQGHKIALRDL 60
           MSTDTSASQASAPRYIMMNDTDNVAIVVNDGGLPAGTVFPDGLTLVDRVPQGHKIALRDL
Sbjct: 1   MSTDTSASQASAPRYIMMNDTDNVAIVVNDGGLPAGTVFPDGLTLVDRVPQGHKIALRDL 60

Query: 61  KQGEAIVRYDVAIGYAVRDIPKGGWIEESLVQMPPARELDNLPIATKKPAPQPPLEGYTF 120
           KQGEAIVRYDVAIGYAVRDIPKGGWIEESLVQMPPARELDNLPIATKKPAPQPPLEGYTF
Sbjct: 61  KQGEAIVRYDVAIGYAVRDIPKGGWIEESLVQMPPARELDNLPIATKKPAPQPPLEGYTF 120

Query: 121 EGYRNADGSVGTRNLLAITTTVQCVAGVVEHAVKRIRAELLPKYPNVEDVVALEHTYGCG 180
           EGYRNADGSVGTRNLLAITTTVQCVAGVVEHAVKRIRAELLPKYPNVEDVVALEHTYGCG
Sbjct: 121 EGYRNADGSVGTRNLLAITTTVQCVAGVVEHAVKRIRAELLPKYPNVEDVVALEHTYGCG 180

Query: 181 VAIDAPNAGIPIRTLRNISLNPNFGGQAMVVSLGCEKLQPNRLLPENMIPIHKQGEPYVV 240
           VAIDAPNAGIPIRTLRNISLNPNFGGQAMVVSLGCEKLQPNRLLPENMIPIHKQGEPYVV
Sbjct: 181 VAIDAPNAGIPIRTLRNISLNPNFGGQAMVVSLGCEKLQPNRLLPENMIPIHKQGEPYVV 240

Query: 241 CLQDAEHVGFNSMIDSIMNMAEARLTELNKRRRETCPASDLVVGVQCGGSDAFSGVTANP 300
           CLQDAEHVGFNSMIDSIMNMAEARLTELNKRRRETCPASDLVVGVQCGGSDAFSGVTANP
Sbjct: 241 CLQDAEHVGFNSMIDSIMNMAEARLTELNKRRRETCPASDLVVGVQCGGSDAFSGVTANP 300

Query: 301 AVGFATDLLVRAGASVMFSEVTEVRDGIDQLTSRAVNEEVAQAMIREMDWYDNYLKQGGV 360
           AVGFATDLLVRAGASVMFSEVTEVRDGIDQLTSRAVNEEVAQAMIREMDWYDNYLKQGGV
Sbjct: 301 AVGFATDLLVRAGASVMFSEVTEVRDGIDQLTSRAVNEEVAQAMIREMDWYDNYLKQGGV 360

Query: 361 DRSANTTPGNKKGGLANIVEKAMGSIVKSGSSPISGVLSPGDKLQQKGLIYAATPASDFI 420
           DRSANTTPGNKKGGLANIVEKAMGSIVKSGSSPISGVLSPGDKLQQKGLIYAATPASDFI
Sbjct: 361 DRSANTTPGNKKGGLANIVEKAMGSIVKSGSSPISGVLSPGDKLQQKGLIYAATPASDFI 420

Query: 421 CGTLQLAAGMNLHIFTTGRGTPYGLAAVPVIKVATRNDLARRWHDLMDVNAGRIASGEAS 480
           CGTLQLAAGMNLHIFTTGRGTPYGLAAVPVIKVATRNDLARRWHDLMDVNAGRIASGEAS
Sbjct: 421 CGTLQLAAGMNLHIFTTGRGTPYGLAAVPVIKVATRNDLARRWHDLMDVNAGRIASGEAS 480

Query: 481 IEDVGWELFQLMLDVASGKKRTWAEQWKLHNALTLFNPAPVT 522
           IEDVGWELFQLMLDVASGKKRTWAEQWKLHNALTLFNPAPVT
Sbjct: 481 IEDVGWELFQLMLDVASGKKRTWAEQWKLHNALTLFNPAPVT 522


Lambda     K      H
   0.317    0.134    0.397 

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: 1110
Number of extensions: 35
Number of successful extensions: 1
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: 522
Length of database: 522
Length adjustment: 35
Effective length of query: 487
Effective length of database: 487
Effective search space:   237169
Effective search space used:   237169
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: 52 (24.6 bits)

Align candidate HSERO_RS15800 HSERO_RS15800 (D-galactarate dehydratase)
to HMM TIGR03248 (garD: galactarate dehydratase (EC 4.2.1.42))

# 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/TIGR03248.hmm
# target sequence database:        /tmp/gapView.31090.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR03248  [M=507]
Accession:   TIGR03248
Description: galactar-dH20: galactarate dehydratase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                  -----------
   8.2e-290  947.4   0.2   9.2e-290  947.2   0.2    1.0  1  lcl|FitnessBrowser__HerbieS:HSERO_RS15800  HSERO_RS15800 D-galactarate dehy


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__HerbieS:HSERO_RS15800  HSERO_RS15800 D-galactarate dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  947.2   0.2  9.2e-290  9.2e-290       2     507 .]      15     522 .]      14     522 .] 0.99

  Alignments for each domain:
  == domain 1  score: 947.2 bits;  conditional E-value: 9.2e-290
                                  TIGR03248   2 yirvneqdnvaivvndkGlpagtefedgltlvekipqghkvalvdlekgdaiirygeviGyavkdiar 69 
                                                yi +n++dnvaivvnd Glpagt+f+dgltlv+++pqghk+al dl++g+ai+ry+  iGyav+di++
  lcl|FitnessBrowser__HerbieS:HSERO_RS15800  15 YIMMNDTDNVAIVVNDGGLPAGTVFPDGLTLVDRVPQGHKIALRDLKQGEAIVRYDVAIGYAVRDIPK 82 
                                                899***************************************************************** PP

                                  TIGR03248  70 GswvkeellelpsapaleelplatkvpeklapleGytfeGyrnadGsvGtknilgittsvqcvagvvd 137
                                                G w++e+l+++p a +l++lp+atk+p++++pleGytfeGyrnadGsvGt+n+l+itt+vqcvagvv+
  lcl|FitnessBrowser__HerbieS:HSERO_RS15800  83 GGWIEESLVQMPPARELDNLPIATKKPAPQPPLEGYTFEGYRNADGSVGTRNLLAITTTVQCVAGVVE 150
                                                ******************************************************************** PP

                                  TIGR03248 138 yavkrikkellpkypnvddvvalnhsyGcGvaidapdaivpirtlrnlalnpnlGGealvvglGcekl 205
                                                +avkri++ellpkypnv+dvval+h+yGcGvaidap+a +pirtlrn++lnpn+GG+a+vv+lGcekl
  lcl|FitnessBrowser__HerbieS:HSERO_RS15800 151 HAVKRIRAELLPKYPNVEDVVALEHTYGCGVAIDAPNAGIPIRTLRNISLNPNFGGQAMVVSLGCEKL 218
                                                ******************************************************************** PP

                                  TIGR03248 206 qperllpeelsave.lkdaavlrlqdekl.GfaemveailelaeerlkklnarkretvpaselvvGlq 271
                                                qp+rllpe++++++ + ++ v++lqd+++ Gf++m+++i+++ae rl++ln+r+ret+pas+lvvG+q
  lcl|FitnessBrowser__HerbieS:HSERO_RS15800 219 QPNRLLPENMIPIHkQGEPYVVCLQDAEHvGFNSMIDSIMNMAEARLTELNKRRRETCPASDLVVGVQ 286
                                                **********9976156999********99************************************** PP

                                  TIGR03248 272 cGGsdafsGvtanpavGfaadllvraGatvlfsevtevrdaihlltpraedaevakaliremkwydey 339
                                                cGGsdafsGvtanpavGfa+dllvraGa+v+fsevtevrd+i++lt+ra ++eva+a+irem+wyd+y
  lcl|FitnessBrowser__HerbieS:HSERO_RS15800 287 CGGSDAFSGVTANPAVGFATDLLVRAGASVMFSEVTEVRDGIDQLTSRAVNEEVAQAMIREMDWYDNY 354
                                                ******************************************************************** PP

                                  TIGR03248 340 larGeadrsanttpGnkkGGlsnivekalGsivksGssaivevlspGekvkkkGliyaatpasdfvcG 407
                                                l++G +drsanttpGnkkGGl+niveka+GsivksGss+i++vlspG+k ++kGliyaatpasdf+cG
  lcl|FitnessBrowser__HerbieS:HSERO_RS15800 355 LKQGGVDRSANTTPGNKKGGLANIVEKAMGSIVKSGSSPISGVLSPGDKLQQKGLIYAATPASDFICG 422
                                                ******************************************************************** PP

                                  TIGR03248 408 tlqlasglnlhvfttGrGtpyGlalvpvikvstrtelaerwadlidldaGriatGeatiedvGwelfr 475
                                                tlqla+g+nlh+fttGrGtpyGla+vpvikv+tr++la+rw+dl+d++aGria+Gea+iedvGwelf+
  lcl|FitnessBrowser__HerbieS:HSERO_RS15800 423 TLQLAAGMNLHIFTTGRGTPYGLAAVPVIKVATRNDLARRWHDLMDVNAGRIASGEASIEDVGWELFQ 490
                                                ******************************************************************** PP

                                  TIGR03248 476 lildvasGrkktwaekyklhndlalfnpapvt 507
                                                l+ldvasG+k+twae++klhn+l+lfnpapvt
  lcl|FitnessBrowser__HerbieS:HSERO_RS15800 491 LMLDVASGKKRTWAEQWKLHNALTLFNPAPVT 522
                                                *******************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (507 nodes)
Target sequences:                          1  (522 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.03
# Mc/sec: 8.78
//
[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