Alignments for a candidate for kbl in Bacteroides thetaiotaomicron VPI-5482

GapMind for catabolism of small carbon sources

Alignments for a candidate for kbl in Bacteroides thetaiotaomicron VPI-5482

Align 2-amino-3-ketobutyrate coenzyme A ligase (EC 2.3.1.29) (characterized)
to candidate 350899 BT1371 2-amino-3-ketobutyrate coenzyme A ligase (NCBI ptt file)

Query= reanno::ANA3:7026975
         (397 letters)



>FitnessBrowser__Btheta:350899
          Length = 395

 Score =  468 bits (1203), Expect = e-136
 Identities = 237/388 (61%), Positives = 292/388 (75%), Gaps = 2/388 (0%)

Query: 10  INQQLADVKAEGLYKSERVIASPQQTAIQVNHQEVVNFCANNYLGLANHPELIKAAQQGL 69
           ++Q LA++K  GLYK ER+I S QQ AI V  +EV+NFCANNYLGL+NHP LIKA+Q+ +
Sbjct: 9   LSQTLAEIKEAGLYKEERLIESAQQAAITVKGKEVLNFCANNYLGLSNHPRLIKASQEMM 68

Query: 70  DSHGFGMASVRFICGTQDIHKQLEASLSEFLGMEDTILYSSCFDANAGLFETLLDAEDAI 129
           +  GFGM+SVRFICGTQDIHK+LEA++S++   EDTILY++CFDAN G+FE L   EDAI
Sbjct: 69  ERRGFGMSSVRFICGTQDIHKELEAAISDYFQTEDTILYAACFDANGGVFEPLFSEEDAI 128

Query: 130 ISDALNHASIIDGVRLCKAKRFRYANNDMADLETQLIAAKAAGARNILIATDGVFSMDGV 189
           ISD+LNHASIIDGVRLCKAKR+RYAN DM DLE  L  A+A   R  ++ TDGVFSMDG 
Sbjct: 129 ISDSLNHASIIDGVRLCKAKRYRYANADMKDLERCLQEAQAQRFR--IVVTDGVFSMDGN 186

Query: 190 IANLQGVCDLADKYGALVMVDDSHAVGFVGLNGRGSHEHCGVMGRVDIITGTLGKALGGA 249
           +A +  +CDLA+KY ALVMVD+SH+ G VG  G G  E     GRVDI TGTLGKA GGA
Sbjct: 187 VAPMDQICDLAEKYDALVMVDESHSAGVVGATGHGVSELYKTYGRVDIYTGTLGKAFGGA 246

Query: 250 SGGFTSGKKEVIDWLRQRSRPYLFSNSLAPSIVTASIHVLEMLKSGQALREAVWENSRYF 309
            GGFT+G+KE+ID LRQRSRPYLFSNSLAP I+ AS+ V +MLK   AL + + EN  YF
Sbjct: 247 LGGFTTGRKEIIDLLRQRSRPYLFSNSLAPGIIGASLEVFKMLKESNALHDKLVENVNYF 306

Query: 310 REKMSAAGFTLGGADHAIIPVMIGDAKLASDFANRLLAEHIYVIGFSFPVVPKGQARIRT 369
           R++M+AAGF +     AI  VM+ DAKL+  +A R+  E IYV GF +PVVPK QARIR 
Sbjct: 307 RDQMTAAGFDIKPTQSAICAVMLHDAKLSQIYAARMQEEGIYVTGFYYPVVPKEQARIRV 366

Query: 370 QMSAAHTREQLDKAIEAFTRIAKEMAII 397
           Q+SA H +  LDK I AF ++ KE+  +
Sbjct: 367 QISAGHEKAHLDKCIAAFIKVGKELGTL 394


Lambda     K      H
   0.321    0.134    0.385 

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: 429
Number of extensions: 14
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: 397
Length of database: 395
Length adjustment: 31
Effective length of query: 366
Effective length of database: 364
Effective search space:   133224
Effective search space used:   133224
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 50 (23.9 bits)

Align candidate 350899 BT1371 (2-amino-3-ketobutyrate coenzyme A ligase (NCBI ptt file))
to HMM TIGR01822 (kbl: glycine C-acetyltransferase (EC 2.3.1.29))

# 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/TIGR01822.hmm
# target sequence database:        /tmp/gapView.15353.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01822  [M=393]
Accession:   TIGR01822
Description: 2am3keto_CoA: glycine C-acetyltransferase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                          -----------
   1.5e-210  685.0   2.4   1.7e-210  684.8   2.4    1.0  1  lcl|FitnessBrowser__Btheta:350899  BT1371 2-amino-3-ketobutyrate co


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Btheta:350899  BT1371 2-amino-3-ketobutyrate coenzyme A ligase (NCBI ptt file)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  684.8   2.4  1.7e-210  1.7e-210       1     392 [.       5     393 ..       5     394 .. 0.99

  Alignments for each domain:
  == domain 1  score: 684.8 bits;  conditional E-value: 1.7e-210
                          TIGR01822   1 lkailaaelesireaGlfkkeriitspqkadirvadGrevlnfcannylGlsdhpeviqaakdaldehGfGlssvr 76 
                                        +k++l++ l  i+eaGl+k+er+i s+q+a i+v +G+evlnfcannylGls+hp++i+a+++ ++ +GfG+ssvr
  lcl|FitnessBrowser__Btheta:350899   5 MKEHLSQTLAEIKEAGLYKEERLIESAQQAAITV-KGKEVLNFCANNYLGLSNHPRLIKASQEMMERRGFGMSSVR 79 
                                        688999****************************.9**************************************** PP

                          TIGR01822  77 ficGtqdlhkelekklaeflgtedailyascfdangGlfeallgeedaiisdalnhasiidGvrlckakryryena 152
                                        ficGtqd+hkele++++++++ted+ilya+cfdangG+fe+l++eedaiisd+lnhasiidGvrlckakryry+na
  lcl|FitnessBrowser__Btheta:350899  80 FICGTQDIHKELEAAISDYFQTEDTILYAACFDANGGVFEPLFSEEDAIISDSLNHASIIDGVRLCKAKRYRYANA 155
                                        **************************************************************************** PP

                          TIGR01822 153 dledleaklkearaagarlrliatdGvfsmdGtiapldeicalaekydalvlvdechatGflGatGrGsaelldvl 228
                                        d++dle+ l+ea+a+  r r+++tdGvfsmdG++ap+d+ic+laekydalv+vde+h++G++GatG G++el   +
  lcl|FitnessBrowser__Btheta:350899 156 DMKDLERCLQEAQAQ--RFRIVVTDGVFSMDGNVAPMDQICDLAEKYDALVMVDESHSAGVVGATGHGVSELYKTY 229
                                        ***************..*********************************************************** PP

                          TIGR01822 229 dkvdiitgtlGkalGGasGGfttakkevvellrqrsrpylfsnslapavvgasikvlelleasnelrdklventry 304
                                        ++vdi+tgtlGka+GGa+GGftt++ke+++llrqrsrpylfsnslap ++gas++v+++l++sn l+dklven++y
  lcl|FitnessBrowser__Btheta:350899 230 GRVDIYTGTLGKAFGGALGGFTTGRKEIIDLLRQRSRPYLFSNSLAPGIIGASLEVFKMLKESNALHDKLVENVNY 305
                                        **************************************************************************** PP

                          TIGR01822 305 frekleaaGfdvkpaehaiipvmlydaklaqklaerlleeGiyviGffypvvpkGqarirvqlsaaheeeqldkav 380
                                        fr++++aaGfd+kp+++ai++vml+dakl+q +a+r++eeGiyv+Gf+ypvvpk qarirvq+sa+he+++ldk++
  lcl|FitnessBrowser__Btheta:350899 306 FRDQMTAAGFDIKPTQSAICAVMLHDAKLSQIYAARMQEEGIYVTGFYYPVVPKEQARIRVQISAGHEKAHLDKCI 381
                                        **************************************************************************** PP

                          TIGR01822 381 eafvkvGrelgv 392
                                         af+kvG+elg 
  lcl|FitnessBrowser__Btheta:350899 382 AAFIKVGKELGT 393
                                        *********996 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (393 nodes)
Target sequences:                          1  (395 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 0.01s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 6.63
//
[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