Alignments for a candidate for ilvE in Oleispira antarctica RB-8

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvE in Oleispira antarctica RB-8

Align Probable branched-chain-amino-acid aminotransferase; BCAT; EC 2.6.1.42 (uncharacterized)
to candidate WP_046007640.1 OLEAN_RS00755 branched-chain amino acid aminotransferase

Query= curated2:O86505
         (362 letters)



>NCBI__GCF_000967895.1:WP_046007640.1
          Length = 331

 Score =  203 bits (516), Expect = 6e-57
 Identities = 132/338 (39%), Positives = 174/338 (51%), Gaps = 15/338 (4%)

Query: 29  FGRHFTDHMVTIKWTEGRGWHDGQLVPYAPLSLDPATMVLHYAQEIFEGLKAYRRPDGSV 88
           FG  F   M    + +   W    +VP   L L P   VLHY+   FEGLKA++  DGSV
Sbjct: 4   FGTVFMPKMALASF-DNNSWTASSIVPSDKLELHPGAHVLHYSSTCFEGLKAFKHEDGSV 62

Query: 89  ATFRPEKNGARFQASSRRLGMPELPVDTFIEACDALVAQDEKWVPAHGGEESLYLRPFMI 148
             FR + N  R   SS  L +P +  D   +     V      VP   G  S+Y+RP  I
Sbjct: 63  NVFRMDANIERMSQSSELLSLPAINKDQLAQMIKDAVGLYADEVPTPPG--SMYIRPTHI 120

Query: 149 ATE--VGLGVRPANEYLFIVIASPAGAYFPGGVKPVSIWVSEDRVRAVPGGMGDAKTGGN 206
            TE  +G    P    L  V+ SP G YF GG KP+ + + ED +R  P  MG  K+GGN
Sbjct: 121 GTEPAIGKAAAPTASSLLYVLLSPVGDYFTGGAKPLRLLLEEDGMRCAPH-MGMIKSGGN 179

Query: 207 YAASLLAQAEAAAKGC--DQVCYLDAIERKWVEELGGMNLYFVYGNKIVTPSLTGSILEG 264
           YA S L     A K C  DQ+ +    +   V+E G  N   + GN+I+T +L  + L G
Sbjct: 180 YA-SALGPISRARKECNADQILFCPNGD---VQETGAANFILIDGNEIITKALDSTFLHG 235

Query: 265 VTRDSLLTVARDLGYEAEEGRVSVDQW-QRDSENGTLTEVFACGTAAVITPVGTVKRAGA 323
           VTRDS+LT+ARD G    E   +V +  +R  + GT  E    GTAAV+TPVGT+   G 
Sbjct: 236 VTRDSILTIARDAGMTVTERDFTVAELLERAKKPGT--EAALSGTAAVLTPVGTLIHNGQ 293

Query: 324 QWQQSGGETGEVTQRLRDALLDIQRGTVADPHGWMHTL 361
           ++    GE GE T +LR AL DIQ G   D +GW+ T+
Sbjct: 294 EFTVGSGEPGETTNKLRQALNDIQWGKAEDKYGWLETI 331


Lambda     K      H
   0.318    0.135    0.413 

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: 379
Number of extensions: 18
Number of successful extensions: 6
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: 362
Length of database: 331
Length adjustment: 29
Effective length of query: 333
Effective length of database: 302
Effective search space:   100566
Effective search space used:   100566
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_046007640.1 OLEAN_RS00755 (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.913691.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   3.4e-103  330.9   0.0   3.8e-103  330.7   0.0    1.0  1  NCBI__GCF_000967895.1:WP_046007640.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000967895.1:WP_046007640.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  330.7   0.0  3.8e-103  3.8e-103       1     311 [.      22     329 ..      22     331 .] 0.97

  Alignments for each domain:
  == domain 1  score: 330.7 bits;  conditional E-value: 3.8e-103
                             TIGR01123   1 WdeaelaseaeleldegsavlhYgqevfeGlkayRtadGkillfRpdanakRlrrsaerlllPeleeelflea 73 
                                           W ++ ++++++lel++g++vlhY++ +feGlka++++dG++++fR dan++R+ +s+e l+lP ++++++ + 
  NCBI__GCF_000967895.1:WP_046007640.1  22 WTASSIVPSDKLELHPGAHVLHYSSTCFEGLKAFKHEDGSVNVFRMDANIERMSQSSELLSLPAINKDQLAQM 94 
                                           9999********************************************************************* PP

                             TIGR01123  74 lkqlvkadkdwvpkakseasLYlRPfliatednlGvkaak..eylflvlasPvGaYfkgglapvsifveteyv 144
                                           +k+ v + +d+vp+   + s+Y+RP+ i+te+ +G++aa+  + l++vl+sPvG+Yf gg +p + ++e++ +
  NCBI__GCF_000967895.1:WP_046007640.1  95 IKDAVGLYADEVPT--PPGSMYIRPTHIGTEPAIGKAAAPtaSSLLYVLLSPVGDYFTGGAKPLRLLLEEDGM 165
                                           *************4..469********************9555689*************************** PP

                             TIGR01123 145 RaapkGtGavkvgGnYaasllaqkkaaeqglddvvyldpvekkkieevGaaniflitkdgelvttplsesiLe 217
                                           R+ap+ +G++k gGnYa++l + + a+++  +d+++++p+++  ++e+Gaan++li ++ e++t++l   +L+
  NCBI__GCF_000967895.1:WP_046007640.1 166 RCAPH-MGMIKSGGNYASALGPISRARKECNADQILFCPNGD--VQETGAANFILIDGN-EIITKALDSTFLH 234
                                           *****.***********************************9..*************98.************* PP

                             TIGR01123 218 gvtresllelakdlgleveereiaidel.kaaveaGeivfacGtaavitPvgelkiegkevevkseevGevtk 289
                                           gvtr+s+l++a+d+g++v+er++++ el ++a++ G ++ ++Gtaav+tPvg l ++g+e++v s+e+Ge t+
  NCBI__GCF_000967895.1:WP_046007640.1 235 GVTRDSILTIARDAGMTVTERDFTVAELlERAKKPGTEAALSGTAAVLTPVGTLIHNGQEFTVGSGEPGETTN 307
                                           *************************9972567788999*********************************** PP

                             TIGR01123 290 klrdeltdiqyGkledkegWiv 311
                                           klr++l diq Gk+edk+gW+ 
  NCBI__GCF_000967895.1:WP_046007640.1 308 KLRQALNDIQWGKAEDKYGWLE 329
                                           ********************85 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (313 nodes)
Target sequences:                          1  (331 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 26.75
//
[ok]

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

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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