Alignments for a candidate for leuB in Pedobacter sp. GW460-11-11-14-LB5

GapMind for Amino acid biosynthesis

Alignments for a candidate for leuB in Pedobacter sp. GW460-11-11-14-LB5

Align 3-isopropylmalate dehydrogenase (EC 1.1.1.85) (characterized)
to candidate CA265_RS15850 CA265_RS15850 3-isopropylmalate dehydrogenase

Query= BRENDA::Q9SA14
         (404 letters)



>FitnessBrowser__Pedo557:CA265_RS15850
          Length = 363

 Score =  353 bits (906), Expect = e-102
 Identities = 184/362 (50%), Positives = 253/362 (69%), Gaps = 9/362 (2%)

Query: 45  NITLLPGDGIGPEVISVAKNVLQKAGFLQGLEFDFQEMPFGGAALDLVGVPLPEETSTAA 104
           NI ++PGDGIGPEV +  K  L+K   + G EF F+E   G AA+++ G PLP+ET   A
Sbjct: 4   NILVIPGDGIGPEVTTWGKAALEKIAEIFGHEFAFEEALMGHAAIEVTGEPLPDETLEKA 63

Query: 105 KQSDAILLGAIGGYKWDKNEK-HLRPEMGLLNIRRDLNVFANLRPATVLPQLVDASTLKK 163
           +QSDAIL GAIG  K+D +    +RPE GLL IR++L +FANLRP  +  +L+ AS++K 
Sbjct: 64  RQSDAILFGAIGHAKYDNDPSLKVRPEQGLLKIRKELGLFANLRPILLFDELLQASSIKP 123

Query: 164 EVAQGVDMMIVRELTGGIYFGEPRGITINENGEEVGFNTEIYAAHEIDRIARVAFETARK 223
           E+ +G D++  RELTG +YFGE               +  IY  +E++RIA  A++ A++
Sbjct: 124 EILRGTDILFFRELTGDVYFGEKT----RSEDRNTASDLMIYHRYEVERIAHKAYQAAQQ 179

Query: 224 RRGKLCSVDKANVLDASILWRKRVTALASEYPDVELSHMYVDNAAMQLVRDPKQFDTIVT 283
           R  +LCSVDKANVL++S LWR+ V  +A +YPDVE  HM++DNAAMQL+++PK+FD ++T
Sbjct: 180 RNKRLCSVDKANVLESSRLWRETVQEIAKQYPDVETEHMFIDNAAMQLIKNPKKFDVVLT 239

Query: 284 NNIFGDILSDEASMITGSIGMLPSASLGESGPGLFEPIHGSAPDIAGQDKANPLATILSA 343
            N+FGDIL+DEAS I GS+GML SAS+GES  G FEPIHGSA DIAG+D ANPLA+ILSA
Sbjct: 240 ANLFGDILTDEASQIAGSMGMLASASVGES-TGFFEPIHGSAHDIAGKDLANPLASILSA 298

Query: 344 AMLLKYGLGEEKAAKMIEDAVVDALNKGFRTGDIYSPGN---KLVGCKEMGEEVLKSVDS 400
           A++L+ G G ++ AK++ D +   L +GFRT DI        K++G  EMG+ VLK +  
Sbjct: 299 ALMLEIGFGLKEEAKLLVDTIDQVLKEGFRTHDIADQSTNRFKVLGTAEMGKLVLKFLSQ 358

Query: 401 KV 402
           K+
Sbjct: 359 KL 360


Lambda     K      H
   0.317    0.136    0.389 

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: 394
Number of extensions: 14
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: 404
Length of database: 363
Length adjustment: 30
Effective length of query: 374
Effective length of database: 333
Effective search space:   124542
Effective search space used:   124542
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: 50 (23.9 bits)

Align candidate CA265_RS15850 CA265_RS15850 (3-isopropylmalate dehydrogenase)
to HMM TIGR00169 (leuB: 3-isopropylmalate dehydrogenase (EC 1.1.1.85))

# 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.aa/TIGR00169.hmm
# target sequence database:        /tmp/gapView.261510.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00169  [M=349]
Accession:   TIGR00169
Description: leuB: 3-isopropylmalate dehydrogenase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                              -----------
   3.1e-140  453.1   0.0   3.5e-140  452.9   0.0    1.0  1  FitnessBrowser__Pedo557:CA265_RS15850  


Domain annotation for each sequence (and alignments):
>> FitnessBrowser__Pedo557:CA265_RS15850  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  452.9   0.0  3.5e-140  3.5e-140       1     339 [.       4     339 ..       4     352 .. 0.97

  Alignments for each domain:
  == domain 1  score: 452.9 bits;  conditional E-value: 3.5e-140
                              TIGR00169   1 kiavLpGDgiGpevvaealkvLkaveerfelklefeealiGGaaidatgePlpeetlkackeadavLlgavG 72 
                                            +i v+pGDgiGpev++   + L++++e f++++ feeal+G aai+ tgePlp+etl++++++da+L+ga+G
  FitnessBrowser__Pedo557:CA265_RS15850   4 NILVIPGDGIGPEVTTWGKAALEKIAEIFGHEFAFEEALMGHAAIEVTGEPLPDETLEKARQSDAILFGAIG 75 
                                            689********************************************************************* PP

                              TIGR00169  73 GpkWdnlpr.dvrPekgLLklrkeldlfanLrPaklfksLeklsplkeeivkgvDlvvvreLtgGiYfGepk 143
                                              k+dn p+ +vrPe+gLLk+rkel+lfanLrP+ lf++L+++s++k+ei +g+D++  reLtg +YfGe++
  FitnessBrowser__Pedo557:CA265_RS15850  76 HAKYDNDPSlKVRPEQGLLKIRKELGLFANLRPILLFDELLQASSIKPEILRGTDILFFRELTGDVYFGEKT 147
                                            ******997589**********************************************************99 PP

                              TIGR00169 144 ereeaeeekkaldtekYtkeeieriarvafelarkrrkkvtsvDkanvLessrlWrktveeiakeyPdvele 215
                                             +e+   +++a d + Y+++e+eria++a+++a++r+k+++svDkanvLessrlWr+tv+eiak+yPdve e
  FitnessBrowser__Pedo557:CA265_RS15850 148 RSED---RNTASDLMIYHRYEVERIAHKAYQAAQQRNKRLCSVDKANVLESSRLWRETVQEIAKQYPDVETE 216
                                            8888...899************************************************************** PP

                              TIGR00169 216 hlyiDnaamqLvksPeqldvvvtsnlfGDilsDeasvitGslGlLPsaslsskglalfepvhgsapdiagkg 287
                                            h++iDnaamqL+k+P+++dvv+t nlfGDil Deas i+Gs+G+L sas++ + +++fep+hgsa diagk+
  FitnessBrowser__Pedo557:CA265_RS15850 217 HMFIDNAAMQLIKNPKKFDVVLTANLFGDILTDEASQIAGSMGMLASASVG-ESTGFFEPIHGSAHDIAGKD 287
                                            ***************************************************.8899**************** PP

                              TIGR00169 288 ianpiaailsaalllryslnleeaaeaieaavkkvleegkrtedlaseatta 339
                                            +anp+a ilsaal+l+ +++l+e+a+ + +++++vl+eg rt+d+a+++t++
  FitnessBrowser__Pedo557:CA265_RS15850 288 LANPLASILSAALMLEIGFGLKEEAKLLVDTIDQVLKEGFRTHDIADQSTNR 339
                                            ***********************************************99764 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (349 nodes)
Target sequences:                          1  (363 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 21.09
//
[ok]

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 2024.

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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
changes to Amino acid biosynthesis since the publication.

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 Amino acid biosynthesis