Alignments for a candidate for garD in Klebsiella michiganensis M5al

GapMind for catabolism of small carbon sources

Alignments for a candidate for garD in Klebsiella michiganensis M5al

Align Galactarate dehydratase (L-threo-forming); GalcD; EC 4.2.1.42 (characterized)
to candidate BWI76_RS24840 BWI76_RS24840 galactarate dehydratase

Query= SwissProt::P39829
         (523 letters)



>FitnessBrowser__Koxy:BWI76_RS24840
          Length = 523

 Score =  988 bits (2553), Expect = 0.0
 Identities = 487/523 (93%), Positives = 510/523 (97%)

Query: 1   MANIEIRQETPTAFYIKVHDTDNVAIIVNDNGLKAGTRFPDGLELIEHIPQGHKVALLDI 60
           MA+IEIRQE+PTAFYIKVH+TDNVAIIVND GL AGTRFPDGL L+EHIPQGHKVAL+DI
Sbjct: 1   MADIEIRQESPTAFYIKVHETDNVAIIVNDRGLTAGTRFPDGLTLVEHIPQGHKVALVDI 60

Query: 61  PANGEIIRYGEVIGYAVRAIPRGSWIDESMVVLPEAPPLHTLPLATKVPEPLPPLEGYTF 120
           P +GEIIRYGEVIGYAVR IP+GSWIDES+V LP+APPLHTLPLATKVP PLPPLEGYTF
Sbjct: 61  PVHGEIIRYGEVIGYAVRDIPQGSWIDESLVELPKAPPLHTLPLATKVPAPLPPLEGYTF 120

Query: 121 EGYRNADGSVGTKNLLGITTSVHCVAGVVDYVVKIIERDLLPKYPNVDGVVGLNHLYGCG 180
           EGYRNADGSVGTKNLLGI+TSVHCVAGVVDYVVKIIERDLLPKYPNVDGVVGLNHLYGCG
Sbjct: 121 EGYRNADGSVGTKNLLGISTSVHCVAGVVDYVVKIIERDLLPKYPNVDGVVGLNHLYGCG 180

Query: 181 VAINAPAAVVPIRTIHNISLNPNFGGEVMVIGLGCEKLQPERLLTGTDDVQAIPVESASI 240
           VAINAPAAVVPIRTIHN++LNPNFGGEVMVIGLGCEKLQPERLL GTDDV+ IPV+SASI
Sbjct: 181 VAINAPAAVVPIRTIHNLALNPNFGGEVMVIGLGCEKLQPERLLEGTDDVKGIPVDSASI 240

Query: 241 VSLQDEKHVGFQSMVEDILQIAERHLQKLNQRQRETCPASELVVGMQCGGSDAFSGVTAN 300
           VSLQDEKHVGF+SMV+DILQ+AERHL+KLNQRQRETCPASELVVGMQCGGSDAFSGVTAN
Sbjct: 241 VSLQDEKHVGFKSMVDDILQVAERHLEKLNQRQRETCPASELVVGMQCGGSDAFSGVTAN 300

Query: 301 PAVGYASDLLVRCGATVMFSEVTEVRDAIHLLTPRAVNEEVGKRLLEEMEWYDNYLNMGK 360
           PAVGYASDLLVRCGATVMFSEVTEVRDAIHLLTPRA+NEEVGKRLLEEM WYDNYL+MGK
Sbjct: 301 PAVGYASDLLVRCGATVMFSEVTEVRDAIHLLTPRAINEEVGKRLLEEMAWYDNYLDMGK 360

Query: 361 TDRSANPSPGNKKGGLANVVEKALGSIAKSGKSAIVEVLSPGQRPTKRGLIYAATPASDF 420
           TDRSANPSPGNKKGGLANVVEKALGSIAKSGKSAI EVLSPGQRPTKRGLIYAATPASDF
Sbjct: 361 TDRSANPSPGNKKGGLANVVEKALGSIAKSGKSAIAEVLSPGQRPTKRGLIYAATPASDF 420

Query: 421 VCGTQQVASGITVQVFTTGRGTPYGLMAVPVIKMATRTELANRWFDLMDINAGTIATGEE 480
           VCGTQQVASGITVQVFTTGRGTPYGL+AVPVIKMATRTELANRW+DLMDINAGTIATGEE
Sbjct: 421 VCGTQQVASGITVQVFTTGRGTPYGLVAVPVIKMATRTELANRWYDLMDINAGTIATGEE 480

Query: 481 TIEEVGWKLFHFILDVASGKKKTFSDQWGLHNQLAVFNPAPVT 523
           TIEEVG KLF FILDVASG+KKTFSDQWGLHNQLAVFNPAPVT
Sbjct: 481 TIEEVGLKLFEFILDVASGRKKTFSDQWGLHNQLAVFNPAPVT 523


Lambda     K      H
   0.317    0.136    0.403 

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: 1029
Number of extensions: 29
Number of successful extensions: 3
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: 523
Length of database: 523
Length adjustment: 35
Effective length of query: 488
Effective length of database: 488
Effective search space:   238144
Effective search space used:   238144
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 (21.7 bits)
S2: 52 (24.6 bits)

Align candidate BWI76_RS24840 BWI76_RS24840 (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.29814.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                               -----------
   8.5e-286  934.1   0.1   9.6e-286  933.9   0.1    1.0  1  lcl|FitnessBrowser__Koxy:BWI76_RS24840  BWI76_RS24840 galactarate dehydr


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Koxy:BWI76_RS24840  BWI76_RS24840 galactarate dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  933.9   0.1  9.6e-286  9.6e-286       2     507 .]      15     523 .]      14     523 .] 0.99

  Alignments for each domain:
  == domain 1  score: 933.9 bits;  conditional E-value: 9.6e-286
                               TIGR03248   2 yirvneqdnvaivvndkGlpagtefedgltlvekipqghkvalvdlekgdaiirygeviGyavkdiarGsw 72 
                                             yi+v+e+dnvai+vnd+Gl+agt+f+dgltlve+ipqghkvalvd+    +iirygeviGyav+di++Gsw
  lcl|FitnessBrowser__Koxy:BWI76_RS24840  15 YIKVHETDNVAIIVNDRGLTAGTRFPDGLTLVEHIPQGHKVALVDIPVHGEIIRYGEVIGYAVRDIPQGSW 85 
                                             9********************************************************************** PP

                               TIGR03248  73 vkeellelpsapaleelplatkvpeklapleGytfeGyrnadGsvGtknilgittsvqcvagvvdyavkri 143
                                             ++e+l+elp+ap+l++lplatkvp++l+pleGytfeGyrnadGsvGtkn+lgi tsv+cvagvvdy+vk i
  lcl|FitnessBrowser__Koxy:BWI76_RS24840  86 IDESLVELPKAPPLHTLPLATKVPAPLPPLEGYTFEGYRNADGSVGTKNLLGISTSVHCVAGVVDYVVKII 156
                                             *********************************************************************** PP

                               TIGR03248 144 kkellpkypnvddvvalnhsyGcGvaidapdaivpirtlrnlalnpnlGGealvvglGceklqperllp.. 212
                                             +++llpkypnvd+vv+lnh yGcGvai+ap+a+vpirt++nlalnpn+GGe++v+glGceklqperll+  
  lcl|FitnessBrowser__Koxy:BWI76_RS24840 157 ERDLLPKYPNVDGVVGLNHLYGCGVAINAPAAVVPIRTIHNLALNPNFGGEVMVIGLGCEKLQPERLLEgt 227
                                             *******************************************************************9622 PP

                               TIGR03248 213 eelsavelkdaavlrlqdekl.GfaemveailelaeerlkklnarkretvpaselvvGlqcGGsdafsGvt 282
                                             ++++ + ++ a++++lqdek+ Gf++mv++il++ae++l+kln+r+ret+paselvvG+qcGGsdafsGvt
  lcl|FitnessBrowser__Koxy:BWI76_RS24840 228 DDVKGIPVDSASIVSLQDEKHvGFKSMVDDILQVAERHLEKLNQRQRETCPASELVVGMQCGGSDAFSGVT 298
                                             45556999*************************************************************** PP

                               TIGR03248 283 anpavGfaadllvraGatvlfsevtevrdaihlltpraedaevakaliremkwydeylarGeadrsanttp 353
                                             anpavG+a+dllvr Gatv+fsevtevrdaihlltpra+++ev+k+l++em+wyd+yl++G++drsan++p
  lcl|FitnessBrowser__Koxy:BWI76_RS24840 299 ANPAVGYASDLLVRCGATVMFSEVTEVRDAIHLLTPRAINEEVGKRLLEEMAWYDNYLDMGKTDRSANPSP 369
                                             *********************************************************************** PP

                               TIGR03248 354 GnkkGGlsnivekalGsivksGssaivevlspGekvkkkGliyaatpasdfvcGtlqlasglnlhvfttGr 424
                                             GnkkGGl+n+vekalGsi+ksG sai+evlspG++++k+GliyaatpasdfvcGt+q+asg++++vfttGr
  lcl|FitnessBrowser__Koxy:BWI76_RS24840 370 GNKKGGLANVVEKALGSIAKSGKSAIAEVLSPGQRPTKRGLIYAATPASDFVCGTQQVASGITVQVFTTGR 440
                                             *********************************************************************** PP

                               TIGR03248 425 GtpyGlalvpvikvstrtelaerwadlidldaGriatGeatiedvGwelfrlildvasGrkktwaekyklh 495
                                             GtpyGl +vpvik++trtela+rw dl+d++aG+iatGe+tie+vG +lf++ildvasGrkkt++++++lh
  lcl|FitnessBrowser__Koxy:BWI76_RS24840 441 GTPYGLVAVPVIKMATRTELANRWYDLMDINAGTIATGEETIEEVGLKLFEFILDVASGRKKTFSDQWGLH 511
                                             *********************************************************************** PP

                               TIGR03248 496 ndlalfnpapvt 507
                                             n+la+fnpapvt
  lcl|FitnessBrowser__Koxy:BWI76_RS24840 512 NQLAVFNPAPVT 523
                                             ***********8 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (507 nodes)
Target sequences:                          1  (523 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 0.00s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 12.30
//
[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