Aligments for a candidate for ilvE in Azospirillum brasilense Sp245

GapMind for Amino acid biosynthesis

Aligments for a candidate for ilvE in Azospirillum brasilense Sp245

Align Branched-chain amino acid aminotransferase (EC 2.6.1.42) (characterized)
to candidate AZOBR_RS16425 AZOBR_RS16425 branched-chain amino acid aminotransferase

Query= reanno::psRCH2:GFF445
         (307 letters)



>lcl|FitnessBrowser__azobra:AZOBR_RS16425 AZOBR_RS16425
           branched-chain amino acid aminotransferase
          Length = 290

 Score =  242 bits (618), Expect = 7e-69
 Identities = 130/290 (44%), Positives = 176/290 (60%), Gaps = 7/290 (2%)

Query: 5   DRDGVIWYDGELVQWRDATTHVLTHTLHYGMGVFEGVRAYNTPDGTAIFRLQAHTDRLFD 64
           DRDGVIWYDG LV WRDA  HVL+H LHY   VFEG R YN   GT +F+L  H++RL  
Sbjct: 8   DRDGVIWYDGALVPWRDANLHVLSHGLHYASCVFEGERVYN---GT-VFKLTEHSERLAA 63

Query: 65  SAHIMNMPMPYSKEEINEATRAAVRENNLESAYIRPMVFYGSEGMGLRASGLKVHVIVAA 124
           SA I+   +PYS  EI+ AT   V+      AY+RP+ + GSE MG+ A   ++HV +A 
Sbjct: 64  SARILGFELPYSVAEIDAATNETVKAMGFTDAYVRPVAWRGSEMMGVAAQASRIHVAIAV 123

Query: 125 WHWGAYMGDEALELGIKVRTSSFTRHHVNITMTRAKSNGAYINSMLALQEAISGGADEAL 184
           W W +Y   EA   GIK+  S + R   ++  T +K+ G Y+   L+  EA + G  +AL
Sbjct: 124 WQWPSYFSPEAKMAGIKLTWSRWRRPAPDMAPTASKAAGLYMICTLSKHEAEAEGYQDAL 183

Query: 185 MLDPEGYVAEGSGENIFIIKDGVIYTPEVTACLNGITRGTVLTLAAEHGLKIVEKRITRD 244
           MLD  GY+AE +G N+F++ DG I+TP+    L+GITR TV+ LA   G++++E+ I  D
Sbjct: 184 MLDYRGYLAEATGANLFLVMDGKIHTPKPDCFLDGITRRTVIDLAKARGIEVIERHIQPD 243

Query: 245 EVYIADEAFFTGTAAEVTPIREVDGRAIGIGRRGPITEKLQKAYFDLVTG 294
           E+    E F TGTAAEVTP+ ++       GR   + E L K Y  LV G
Sbjct: 244 ELANTQEVFLTGTAAEVTPVGQIGDHRFTPGR---VCETLVKDYDALVRG 290


Lambda     K      H
   0.319    0.135    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: 266
Number of extensions: 6
Number of successful extensions: 2
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: 307
Length of database: 290
Length adjustment: 27
Effective length of query: 280
Effective length of database: 263
Effective search space:    73640
Effective search space used:    73640
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 48 (23.1 bits)

Align candidate AZOBR_RS16425 AZOBR_RS16425 (branched-chain amino acid aminotransferase)
to HMM TIGR01122 (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/TIGR01122.hmm
# target sequence database:        /tmp/gapView.28778.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01122  [M=298]
Accession:   TIGR01122
Description: ilvE_I: 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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
    1.2e-90  289.6   0.0    1.4e-90  289.5   0.0    1.0  1  lcl|FitnessBrowser__azobra:AZOBR_RS16425  AZOBR_RS16425 branched-chain ami


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__azobra:AZOBR_RS16425  AZOBR_RS16425 branched-chain amino acid aminotransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  289.5   0.0   1.4e-90   1.4e-90       1     285 [.      14     289 ..      14     290 .] 0.96

  Alignments for each domain:
  == domain 1  score: 289.5 bits;  conditional E-value: 1.4e-90
                                 TIGR01122   1 wldGelvdvedakvhvlthalhYGtgvfeGiRaYetdkglaifrlkehveRlydsakilrleipyskee 69 
                                               w+dG lv+++da++hvl+h+lhY + vfeG R+Y++    ++f+l+eh eRl  sa+il +e+pys  e
  lcl|FitnessBrowser__azobra:AZOBR_RS16425  14 WYDGALVPWRDANLHVLSHGLHYASCVFEGERVYNG----TVFKLTEHSERLAASARILGFELPYSVAE 78 
                                               9***********************************....9**************************** PP

                                 TIGR01122  70 lvevtkevlrknnlksaYiRplvyvGaedlglkpkvdlkveviiaawewgaylgeealekGikvkvssf 138
                                               +  +t+e++++ ++++aY+Rp++++G+e +g+ ++++ +++v+ia+w+w+ y+  ea   Gik + s +
  lcl|FitnessBrowser__azobra:AZOBR_RS16425  79 IDAATNETVKAMGFTDAYVRPVAWRGSEMMGVAAQAS-RIHVAIAVWQWPSYFSPEAKMAGIKLTWSRW 146
                                               **********************************655.9****************************** PP

                                 TIGR01122 139 rraavnsiptkakaagnYlnsllaksealraGydeailLdeeGyvaeGsGenifivkdgvlltPpvses 207
                                               rr a+++ pt+ kaag Y+  +l k+ea ++Gy++a++Ld  Gy+ae +G n+f+v dg++ tP+  + 
  lcl|FitnessBrowser__azobra:AZOBR_RS16425 147 RRPAPDMAPTASKAAGLYMICTLSKHEAEAEGYQDALMLDYRGYLAEATGANLFLVMDGKIHTPKP-DC 214
                                               *****************************************************************9.99 PP

                                 TIGR01122 208 iLkgitrdaviklakelgievkeerisreelytaDevfltGtaaevtPirevDgrkigegkrGpvtkkl 276
                                                L+gitr +vi+lak +giev e++i  +el  + evfltGtaaevtP+ ++ + +      G v ++l
  lcl|FitnessBrowser__azobra:AZOBR_RS16425 215 FLDGITRRTVIDLAKARGIEVIERHIQPDELANTQEVFLTGTAAEVTPVGQIGDHRFTP---GRVCETL 280
                                               ****************************************************9998866...5567777 PP

                                 TIGR01122 277 qeaffdlve 285
                                                + +  lv+
  lcl|FitnessBrowser__azobra:AZOBR_RS16425 281 VKDYDALVR 289
                                               777777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (298 nodes)
Target sequences:                          1  (290 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: 6.95
//
[ok]

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 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, or view the source code, or see 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