Alignments for a candidate for ilvE in Echinicola vietnamensis KMM 6221, DSM 17526

GapMind for catabolism of small carbon sources

Alignments for a candidate for ilvE in Echinicola vietnamensis KMM 6221, DSM 17526

Align Branched-chain-amino-acid aminotransferase 2; BCAT 2; Vegetative protein 85; VEG85; EC 2.6.1.42 (characterized)
to candidate Echvi_2202 Echvi_2202 branched-chain amino acid aminotransferase, group II

Query= SwissProt::P39576
         (363 letters)



>FitnessBrowser__Cola:Echvi_2202
          Length = 355

 Score =  334 bits (857), Expect = 2e-96
 Identities = 172/356 (48%), Positives = 239/356 (67%), Gaps = 8/356 (2%)

Query: 5   TIRVELTSTKKPK---PDPNQLSFGRVFTDHMFVMDYAADKGWYDPRIIPYQPLSMDPAA 61
           TI +++  T + K    D   LSFG+V +DHMFV DY   + W D RI PY PLS++PA 
Sbjct: 4   TIDIQIKQTSQSKLQGTDFENLSFGQVMSDHMFVADYKNGE-WQDFRIEPYAPLSLNPAN 62

Query: 62  MVYHYGQTVFEGLKAYVSEDDHVLLFRPEKNMERLNQSNDRLCIPQIDEEQVLEGLKQLV 121
              HYGQ+VFEGLKAY  E ++VL+FRP+ N +RLN+S DRLCIPQ+ EE  +EGL++L+
Sbjct: 63  ATLHYGQSVFEGLKAYKDEHNNVLIFRPDANQQRLNESADRLCIPQLPEEIFMEGLRKLL 122

Query: 122 AIDKDWIPNAEGTSLYIRPFIIATEPFLGVAASHTYKLLIILSPVGSYYKEGIKPVKIAV 181
           A+D+DWIPN  G SLYIRPFI AT+ +LG+  S TYK +I   PVG YY    KPV + V
Sbjct: 123 AVDRDWIPNKPGCSLYIRPFIFATDDYLGIRPSATYKFMIFTCPVGHYY---AKPVSVKV 179

Query: 182 ESEFVRAVKGGTGNAKTAGNYASSLKAQQVAEEKGFSQVLWLDGIEKKYIEEVGSMNIFF 241
           E+++ RA +GGTG AK AGNYA SL   Q+A+++G+ Q+LW DG   + IEE G+MN+ F
Sbjct: 180 ETKYTRAAEGGTGQAKAAGNYAGSLYPAQIAQKQGYDQLLWTDGKNHENIEESGTMNVMF 239

Query: 242 KINGEIVT-PMLNGSILEGITRNSVIALLKHWGLQVSERKIAIDEVIQAHKDGILEEAFG 300
            IN  ++T P   G+IL+GITR+SV+ L K  GL+VSER + + E+ +A ++  L+EAFG
Sbjct: 240 IINNTLITAPTSKGTILKGITRDSVLTLAKEKGLKVSERFLTVTELKEALENNTLQEAFG 299

Query: 301 TGTAAVISPVGELIWQDETLSINNGETGEIAKKLYDTITGIQKGAVADEFGWTTEV 356
           TGTAA I+ + ++   D    +        + ++ +T+  I+ G   D  GW T+V
Sbjct: 300 TGTAATIAHIYKINVGDTDYDLPEKPADSFSYQVLETLDAIKYGRQEDTHGWITKV 355


Lambda     K      H
   0.316    0.135    0.390 

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: 377
Number of extensions: 14
Number of successful extensions: 4
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: 363
Length of database: 355
Length adjustment: 29
Effective length of query: 334
Effective length of database: 326
Effective search space:   108884
Effective search space used:   108884
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 Echvi_2202 Echvi_2202 (branched-chain amino acid aminotransferase, group II)
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.3799605.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                        -----------
   1.1e-107  345.6   0.0   1.3e-107  345.4   0.0    1.0  1  FitnessBrowser__Cola:Echvi_2202  


Domain annotation for each sequence (and alignments):
>> FitnessBrowser__Cola:Echvi_2202  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  345.4   0.0  1.3e-107  1.3e-107       1     313 []      45     355 .]      45     355 .] 0.97

  Alignments for each domain:
  == domain 1  score: 345.4 bits;  conditional E-value: 1.3e-107
                        TIGR01123   1 WdeaelaseaeleldegsavlhYgqevfeGlkayRtadGkillfRpdanakRlrrsaerlllPeleeelflealkqlv 78 
                                      W++ +++++a+l+l+++ a lhYgq vfeGlkay+ +  ++l+fRpdan +Rl++sa+rl +P+l+ee+f+e l++l+
  FitnessBrowser__Cola:Echvi_2202  45 WQDFRIEPYAPLSLNPANATLHYGQSVFEGLKAYKDEHNNVLIFRPDANQQRLNESADRLCIPQLPEEIFMEGLRKLL 122
                                      9***************************************************************************** PP

                        TIGR01123  79 kadkdwvpkakseasLYlRPfliatednlGvkaakeylflvlasPvGaYfkgglapvsifveteyvRaapkGtGavkv 156
                                      ++d+dw+p++  + sLY+RPf++at+d+lG++++ +y f+++++PvG+Y+++   pvs+ vet+y+Raa++GtG++k 
  FitnessBrowser__Cola:Echvi_2202 123 AVDRDWIPNKP-GCSLYIRPFIFATDDYLGIRPSATYKFMIFTCPVGHYYAK---PVSVKVETKYTRAAEGGTGQAKA 196
                                      ********777.**************************************86...56679****************** PP

                        TIGR01123 157 gGnYaasllaqkkaaeqglddvvyldpvekkkieevGaaniflitkdgelvttpls.esiLegvtresllelakdlgl 233
                                      +GnYa sl + ++a++qg+d+ ++ d +++++iee G++n+++i+++ +l+t p s + iL+g+tr+s+l+lak+ gl
  FitnessBrowser__Cola:Echvi_2202 197 AGNYAGSLYPAQIAQKQGYDQLLWTDGKNHENIEESGTMNVMFIINN-TLITAPTSkGTILKGITRDSVLTLAKEKGL 273
                                      **********************************************9.88888877368******************* PP

                        TIGR01123 234 eveereiaidelkaaveaGei..vfacGtaavitPvgelkiegkevevkseevGevtkklrdeltdiqyGkledkegW 309
                                      +v+er +++ elk+a e+  +  +f++Gtaa i+ + +++++++ + + +++    ++++ ++l  i+yG++ed++gW
  FitnessBrowser__Cola:Echvi_2202 274 KVSERFLTVTELKEALENNTLqeAFGTGTAATIAHIYKINVGDTDYDLPEKPADSFSYQVLETLDAIKYGRQEDTHGW 351
                                      ******************98888******************************************************* PP

                        TIGR01123 310 ivev 313
                                      i++v
  FitnessBrowser__Cola:Echvi_2202 352 ITKV 355
                                      *997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (313 nodes)
Target sequences:                          1  (355 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: 18.38
//
[ok]

This GapMind analysis is from Apr 09 2024. 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