GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvE in Azospirillum brasilense Sp245

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

Query= BRENDA::O86428
         (307 letters)



>FitnessBrowser__azobra:AZOBR_RS16425
          Length = 290

 Score =  243 bits (619), Expect = 5e-69
 Identities = 129/290 (44%), Positives = 178/290 (61%), Gaps = 7/290 (2%)

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

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

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

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

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


Lambda     K      H
   0.319    0.134    0.394 

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: 267
Number of extensions: 9
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.19034.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: 7.73
//
[ok]

This GapMind analysis is from Apr 09 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:

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