Alignments for a candidate for ilvE in Stenotrophomonas chelatiphaga DSM 21508

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvE in Stenotrophomonas chelatiphaga DSM 21508

Align branched-chain-amino-acid transaminase (EC 2.6.1.42) (characterized)
to candidate WP_042613067.1 ABB28_RS07920 branched-chain amino acid aminotransferase

Query= BRENDA::A0R066
         (368 letters)



>NCBI__GCF_001431535.1:WP_042613067.1
          Length = 364

 Score =  424 bits (1090), Expect = e-123
 Identities = 208/367 (56%), Positives = 268/367 (73%), Gaps = 4/367 (1%)

Query: 1   MNSGPLEFTVSANTNPATDAVRESILANPGFGKYYTDHMVSIDYTVDEGWHNAQVIPYGP 60
           M+   + F V+ + +P +   R +IL  PGFG ++TDHMV + +  D GWHNA V PYGP
Sbjct: 1   MSQSNISFDVTRSAHPRSADERAAILEKPGFGLHFTDHMVEVRWDKDTGWHNANVRPYGP 60

Query: 61  IQLDPSAIVLHYGQEIFEGLKAYRWADGSIVSFRPEANAARLQSSARRLAIPELPEEVFI 120
           + LDP+A VLHYGQEIFEG+KAYR ADGS+ +FRP+AN  RLQ SA+RLA+PELP ++F+
Sbjct: 61  LLLDPAAAVLHYGQEIFEGIKAYRHADGSVWTFRPDANGRRLQRSAQRLALPELPVDIFV 120

Query: 121 ESLRQLIAVDEKWVPPAGGEESLYLRPFVIATEPGLGVRPSNEYRYLLIASPAGAYFKGG 180
           ESL+QL+A+D+ WVP A  E SLY RPF+I  E  LGVR +++  Y +IASPAG YF  G
Sbjct: 121 ESLKQLVALDKDWVPSA-DESSLYFRPFMIGDEAFLGVRGAHKAGYYVIASPAGPYFAKG 179

Query: 181 IKPVSVWLSHEYVRASPGGTGAAKFGGNYAASLLAQAQAAEMGCDQVVWLDAIERRYVEE 240
           + PVS+WLS EY RA+ GGTGAAK GGNYAASLL Q +A   GC QV++LD  E +Y+EE
Sbjct: 180 VAPVSIWLSTEYARAAKGGTGAAKCGGNYAASLLPQQKAQAQGCSQVLFLDPTEGKYLEE 239

Query: 241 MGGMNLFFVFGSGGSARLVTPELSGSLLPGITRDSLLQLATDAGFAVEERKIDVDEWQKK 300
           +GGMN+F V+  G    LVTP+LSGS+L GITR+S+LQLA D G  VEERK+ +DEW++ 
Sbjct: 240 LGGMNVFLVYKDG---TLVTPQLSGSILEGITRESILQLARDRGMKVEERKVSIDEWKQG 296

Query: 301 AGAGEITEVFACGTAAVITPVSHVKHHDGEFTIADGQPGEITMALRDTLTGIQRGTFADT 360
             +GEITEVFACGTAAV+TP+  +K    E    +   GE+T++LR  LT IQ G   D 
Sbjct: 297 VASGEITEVFACGTAAVVTPIGQLKGEGFEVGDINAPAGEVTLSLRKELTDIQYGRLPDR 356

Query: 361 HGWMARL 367
           HGW+ +L
Sbjct: 357 HGWLVKL 363


Lambda     K      H
   0.318    0.135    0.409 

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: 465
Number of extensions: 12
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: 368
Length of database: 364
Length adjustment: 30
Effective length of query: 338
Effective length of database: 334
Effective search space:   112892
Effective search space used:   112892
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: 49 (23.5 bits)

Align candidate WP_042613067.1 ABB28_RS07920 (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.aa/TIGR01123.hmm
# target sequence database:        /tmp/gapView.14402.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.5e-146  473.3   0.0   1.7e-146  473.2   0.0    1.0  1  lcl|NCBI__GCF_001431535.1:WP_042613067.1  ABB28_RS07920 branched-chain ami


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_001431535.1:WP_042613067.1  ABB28_RS07920 branched-chain amino acid aminotransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  473.2   0.0  1.7e-146  1.7e-146       1     313 []      50     363 ..      50     363 .. 1.00

  Alignments for each domain:
  == domain 1  score: 473.2 bits;  conditional E-value: 1.7e-146
                                 TIGR01123   1 WdeaelaseaeleldegsavlhYgqevfeGlkayRtadGkillfRpdanakRlrrsaerlllPeleeel 69 
                                               W++a+++++++l ld+++avlhYgqe+feG+kayR+adG++++fRpdan +Rl+rsa+rl+lPel+ ++
  lcl|NCBI__GCF_001431535.1:WP_042613067.1  50 WHNANVRPYGPLLLDPAAAVLHYGQEIFEGIKAYRHADGSVWTFRPDANGRRLQRSAQRLALPELPVDI 118
                                               ********************************************************************* PP

                                 TIGR01123  70 flealkqlvkadkdwvpkakseasLYlRPfliatednlGvkaakeylflvlasPvGaYfkgglapvsif 138
                                               f+e+lkqlv++dkdwvp+a+ e+sLY+RPf+i+ e+ lGv++a+++ ++v+asP+G+Yf++g+apvsi+
  lcl|NCBI__GCF_001431535.1:WP_042613067.1 119 FVESLKQLVALDKDWVPSAD-ESSLYFRPFMIGDEAFLGVRGAHKAGYYVIASPAGPYFAKGVAPVSIW 186
                                               *****************999.************************************************ PP

                                 TIGR01123 139 veteyvRaapkGtGavkvgGnYaasllaqkkaaeqglddvvyldpvekkkieevGaaniflitkdgelv 207
                                               ++tey+Raa++GtGa+k+gGnYaasll+q+ka++qg+++v++ldp+e k++ee+G++n+fl++kdg+lv
  lcl|NCBI__GCF_001431535.1:WP_042613067.1 187 LSTEYARAAKGGTGAAKCGGNYAASLLPQQKAQAQGCSQVLFLDPTEGKYLEELGGMNVFLVYKDGTLV 255
                                               ********************************************************************* PP

                                 TIGR01123 208 ttplsesiLegvtresllelakdlgleveereiaidelkaaveaGei..vfacGtaavitPvgelkieg 274
                                               t++ls+siLeg+tres+l+la+d+g++veer+++ide+k+ v++Gei  vfacGtaav+tP+g+lk eg
  lcl|NCBI__GCF_001431535.1:WP_042613067.1 256 TPQLSGSILEGITRESILQLARDRGMKVEERKVSIDEWKQGVASGEIteVFACGTAAVVTPIGQLKGEG 324
                                               **********************************************999******************** PP

                                 TIGR01123 275 kevevkseevGevtkklrdeltdiqyGkledkegWivev 313
                                                ev   +++ Gevt +lr+eltdiqyG+l d++gW+v++
  lcl|NCBI__GCF_001431535.1:WP_042613067.1 325 FEVGDINAPAGEVTLSLRKELTDIQYGRLPDRHGWLVKL 363
                                               ************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (313 nodes)
Target sequences:                          1  (364 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: 00:00:00.01
# Mc/sec: 7.36
//
[ok]

This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 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