GapMind for Amino acid biosynthesis

 

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.aa/TIGR01123.hmm
# target sequence database:        /tmp/gapView.2614539.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 0.00s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 20.73
//
[ok]

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

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:

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:

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:

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