Alignments for a candidate for ilvE in Flavobacterium beibuense F44-8

GapMind for catabolism of small carbon sources

Alignments for a candidate for ilvE in Flavobacterium beibuense F44-8

Align Branched-chain-amino-acid transaminase 1; BCAT 1; EC 2.6.1.42 (characterized)
to candidate WP_052123371.1 Q763_RS09440 branched-chain amino acid aminotransferase

Query= SwissProt::O31461
         (356 letters)



>NCBI__GCF_000769915.1:WP_052123371.1
          Length = 349

 Score =  285 bits (728), Expect = 2e-81
 Identities = 147/331 (44%), Positives = 210/331 (63%), Gaps = 10/331 (3%)

Query: 24  FGQYFTDYMFVMDYEEGIGWHHPRIAPYAPLTLDPSSSVFHYGQAVFEGLKAYRTDDGRV 83
           FG   TD++F+ +Y+ G  W   RI P    +L P +   HYGQ VFEG+KA+R D+G+V
Sbjct: 23  FGTQPTDHLFLSEYDHG-NWRSHRIVPTQHFSLSPFALCLHYGQTVFEGMKAFRQDNGQV 81

Query: 84  LLFRPDQNIKRLNRSCERMSMPPLDEELVLEALTQLVELEKDWVPKEKGTSLYIRPFVIA 143
            +FRP+++ +R NRS ERM +PP+++EL + AL +LV LE+ W+P++K  SLYIRPFV A
Sbjct: 82  HIFRPEKHHQRFNRSLERMCIPPIEKELFINALEELVRLEQHWIPQDKEVSLYIRPFVFA 141

Query: 144 TEPSLGVKASRSYTFMIVLSPVGSYYGDDQLKPVRIYVEDEYVRAVNGGVGFAKTAGNYA 203
           TE  LGVK + +YTF I  +P+G YY     KPVR+ VE EYVRA  GGVG+ K  GNY 
Sbjct: 142 TESRLGVKVADNYTFCITCTPMGLYYP----KPVRVKVETEYVRAAEGGVGYVKCGGNYG 197

Query: 204 ASLQAQRKANELGYDQVLWLDAIEKKYVEEVGSMNIFFVINGEAVTPALSGSILSGVTRA 263
           A+    ++A E G+DQ++W DA   +++EE G+MN+  ++    +TP LS SIL GVTR 
Sbjct: 198 AAFYPTQQAKEQGFDQIIWTDAKTHQFLEEAGTMNMMVMLKDTLITPRLSTSILDGVTRN 257

Query: 264 SAIELIRSWGIPVREERISIDEVYAASARGELTEVFGTGTAAVVTPVGELNIHGK--TVI 321
           S I++ R  G+ V E  IS  E+  A   G   E+FG GTAAV++PV  + I  K  +  
Sbjct: 258 SIIQIARDKGMKVEERAISYQELEDAFNAGNRVELFGVGTAAVISPVYSIQIQDKDYSPY 317

Query: 322 VGDGQIGDLSKKLYETITDIQLGKVKGPFNW 352
           +GD     +  +L   + +I+ G+ K   +W
Sbjct: 318 IGDDA---MMFQLKTALENIRKGRTKDTHSW 345


Lambda     K      H
   0.317    0.137    0.400 

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: 335
Number of extensions: 7
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: 356
Length of database: 349
Length adjustment: 29
Effective length of query: 327
Effective length of database: 320
Effective search space:   104640
Effective search space used:   104640
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: 49 (23.5 bits)

Align candidate WP_052123371.1 Q763_RS09440 (branched-chain amino acid aminotransferase)
to HMM TIGR01123 (ilvE: branched-chain amino acid aminotransferase (EC 2.6.1.42))

# 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/TIGR01123.hmm
# target sequence database:        /tmp/gapView.1506074.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01123  [M=313]
Accession:   TIGR01123
Description: ilvE_II: branched-chain amino acid aminotransferase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   7.8e-106  339.5   0.0   8.8e-106  339.4   0.0    1.0  1  NCBI__GCF_000769915.1:WP_052123371.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000769915.1:WP_052123371.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  339.4   0.0  8.8e-106  8.8e-106       1     309 [.      41     345 ..      41     349 .] 0.97

  Alignments for each domain:
  == domain 1  score: 339.4 bits;  conditional E-value: 8.8e-106
                             TIGR01123   1 WdeaelaseaeleldegsavlhYgqevfeGlkayRtadGkillfRpdanakRlrrsaerlllPeleeelflea 73 
                                           W + ++++ ++++l++ +  lhYgq vfeG+ka+R+++G++ +fRp++  +R++rs er+ +P +e+elf++a
  NCBI__GCF_000769915.1:WP_052123371.1  41 WRSHRIVPTQHFSLSPFALCLHYGQTVFEGMKAFRQDNGQVHIFRPEKHHQRFNRSLERMCIPPIEKELFINA 113
                                           9999********************************************************************* PP

                             TIGR01123  74 lkqlvkadkdwvpkakseasLYlRPfliatednlGvkaakeylflvlasPvGaYfkgglapvsifveteyvRa 146
                                           l++lv+++++w+p+ k e sLY+RPf++ate  lGvk a +y+f++ ++P+G Y+ +   pv++ veteyvRa
  NCBI__GCF_000769915.1:WP_052123371.1 114 LEELVRLEQHWIPQDK-EVSLYIRPFVFATESRLGVKVADNYTFCITCTPMGLYYPK---PVRVKVETEYVRA 182
                                           *************877.**************************************86...56669******** PP

                             TIGR01123 147 apkGtGavkvgGnYaasllaqkkaaeqglddvvyldpvekkkieevGaaniflitkdgelvttplsesiLegv 219
                                           a++G+G vk+gGnY a++ + ++a+eqg+d++++ d+++++ +ee+G++n+++++kd +l+t+ ls siL+gv
  NCBI__GCF_000769915.1:WP_052123371.1 183 AEGGVGYVKCGGNYGAAFYPTQQAKEQGFDQIIWTDAKTHQFLEEAGTMNMMVMLKD-TLITPRLSTSILDGV 254
                                           *********************************************************.*************** PP

                             TIGR01123 220 tresllelakdlgleveereiaidelkaaveaGei..vfacGtaavitPvgelkiegkevevkseevGevtkk 290
                                           tr+s++++a+d g++veer i+ +el++a +aG+    f++Gtaavi+Pv +++i++k ++ + +    +  +
  NCBI__GCF_000769915.1:WP_052123371.1 255 TRNSIIQIARDKGMKVEERAISYQELEDAFNAGNRveLFGVGTAAVISPVYSIQIQDKDYSPYIG-DDAMMFQ 326
                                           *********************************98778********************9987766.3467889 PP

                             TIGR01123 291 lrdeltdiqyGkledkegW 309
                                           l+ +l +i  G+++d++ W
  NCBI__GCF_000769915.1:WP_052123371.1 327 LKTALENIRKGRTKDTHSW 345
                                           ******************* PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (313 nodes)
Target sequences:                          1  (349 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: 00:00:00.00
# Mc/sec: 12.51
//
[ok]

This GapMind analysis is from Sep 24 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 2024 update 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