Alignments for a candidate for leuC in Azospirillum brasilense Sp245

GapMind for Amino acid biosynthesis

Alignments for a candidate for leuC in Azospirillum brasilense Sp245

Align 3-isopropylmalate dehydratase large subunit; Alpha-IPM isomerase; IPMI; Isopropylmalate isomerase; EC 4.2.1.33 (characterized)
to candidate AZOBR_RS27815 AZOBR_RS27815 isopropylmalate isomerase

Query= SwissProt::Q7TXH6
         (473 letters)



>FitnessBrowser__azobra:AZOBR_RS27815
          Length = 471

 Score =  530 bits (1365), Expect = e-155
 Identities = 262/459 (57%), Positives = 327/459 (71%), Gaps = 1/459 (0%)

Query: 8   PRTLAEKIWDDHIVVSGGGCAPDLIYIDLHLVHEVTSPQAFDGLRLAGRRVRRPELTLAT 67
           PR++ +KIWD H+V   G     L++ID H++HEVTSPQA+ GL  AGRR+RRP+LT AT
Sbjct: 4   PRSIIDKIWDQHVVADLGD-GRVLLHIDRHMLHEVTSPQAYAGLAAAGRRLRRPDLTFAT 62

Query: 68  EDHNVPTVDIDQPIADPVSRTQVETLRRNCAEFGIRLHSMGDIEQGIVHVVGPQLGLTQP 127
            DH V T +       P     +  LR N    G+ L  +GD+ QGIVHV+ P+LG+  P
Sbjct: 63  ADHIVSTENGRTDDTVPGGPEMIRALRANAEATGVALFDLGDVRQGIVHVIAPELGIALP 122

Query: 128 GMTIVCGDSHTSTHGAFGALAMGIGTSEVEHVLATQTLPLRPFKTMAVNVDGRLPDGVSA 187
           G T+VCGDSHTST GA GA+A GIGTSEVEHV+ATQT  LR   TM + V G  P GVSA
Sbjct: 123 GATLVCGDSHTSTVGALGAMAWGIGTSEVEHVMATQTAILRRPPTMRITVSGTRPAGVSA 182

Query: 188 KDIILALIAKIGTGGGQGHVIEYRGSAIESLSMEGRMTICNMSIEAGARAGMVAPDETTY 247
           KD++L LIA IGT G  G+ +EY G AI +LSME RMT+CNMS+E GAR G++APDE T+
Sbjct: 183 KDMVLKLIATIGTAGATGYGVEYAGPAIRALSMEERMTVCNMSVELGARFGLIAPDEVTF 242

Query: 248 AFLRGRPHAPTGAQWDTALVYWQRLRTDVGAVFDTEVYLDAASLSPFVTWGTNPGQGVPL 307
           A+L+GRP AP GA W+ A+V W+ L +D GA FD E+ LD +SL+P V+WGT+P   + +
Sbjct: 243 AYLQGRPFAPAGALWEQAVVAWRALASDPGARFDAEIELDVSSLTPQVSWGTSPQDCIGV 302

Query: 308 AAAVPDPQLMTDDAERQAAEKALAYMDLRPGTAMREIAVDAVFVGSCTNGRIEDLRVVAE 367
              VPDP+   D   RQA  +AL Y+ L PGT +R++ VD VF+GSCTN RIEDLR  A 
Sbjct: 303 GETVPDPEREADPKRRQAMRRALDYIGLEPGTPIRDLPVDMVFIGSCTNSRIEDLRAAAA 362

Query: 368 VLRGRKVADGVRMLIVPGSMRVRAQAEAEGLGEIFTDAGAQWRQAGCSMCLGMNPDQLAS 427
           VL+GR+VA G+R L+VPGS +VR QAEAEGL  +FT AG +WR+ GCSMC GMN D++  
Sbjct: 363 VLKGRRVAAGLRALVVPGSGQVRRQAEAEGLDRVFTAAGFEWREPGCSMCAGMNADRVPP 422

Query: 428 GERCAATSNRNFEGRQGAGGRTHLVSPAVAAATAVRGTL 466
           G+RC ATSNRNFEGRQG G RTHL SPA AAA AV G +
Sbjct: 423 GKRCVATSNRNFEGRQGPGARTHLASPATAAAAAVAGRI 461


Lambda     K      H
   0.319    0.135    0.402 

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: 779
Number of extensions: 41
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: 473
Length of database: 471
Length adjustment: 33
Effective length of query: 440
Effective length of database: 438
Effective search space:   192720
Effective search space used:   192720
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: 51 (24.3 bits)

Align candidate AZOBR_RS27815 AZOBR_RS27815 (isopropylmalate isomerase)
to HMM TIGR00170 (leuC: 3-isopropylmalate dehydratase, large subunit (EC 4.2.1.33))

# 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/TIGR00170.hmm
# target sequence database:        /tmp/gapView.19853.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00170  [M=466]
Accession:   TIGR00170
Description: leuC: 3-isopropylmalate dehydratase, large subunit
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.7e-210  685.4   0.0     2e-210  685.2   0.0    1.0  1  lcl|FitnessBrowser__azobra:AZOBR_RS27815  AZOBR_RS27815 isopropylmalate is


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__azobra:AZOBR_RS27815  AZOBR_RS27815 isopropylmalate isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  685.2   0.0    2e-210    2e-210       1     465 [.       3     466 ..       3     467 .. 0.99

  Alignments for each domain:
  == domain 1  score: 685.2 bits;  conditional E-value: 2e-210
                                 TIGR00170   1 maktlyeklfdahvvkeaenetdllyidrhlvhevtspqafeglraagrkvrrvdktlatldhnistes 69 
                                               m++++++k++d+hvv +  ++  ll+idrh++hevtspqa+ gl aagr++rr+d t+at dh +ste+
  lcl|FitnessBrowser__azobra:AZOBR_RS27815   3 MPRSIIDKIWDQHVVADLGDGRVLLHIDRHMLHEVTSPQAYAGLAAAGRRLRRPDLTFATADHIVSTEN 71 
                                               89******************************************************************* PP

                                 TIGR00170  70 rdveikeekaklqvkeleknvkefgvklfdlssaeqgivhvvgpeegltlpgktivcgdshtathgafg 138
                                                 ++ +       +++l  n++++gv lfdl +++qgivhv+ pe g++lpg t+vcgdsht+t ga+g
  lcl|FitnessBrowser__azobra:AZOBR_RS27815  72 GRTDDTVPGGPEMIRALRANAEATGVALFDLGDVRQGIVHVIAPELGIALPGATLVCGDSHTSTVGALG 140
                                               9888888889999******************************************************** PP

                                 TIGR00170 139 alafgigtsevehvlatqtlkqaraktlkievegklakgitakdiilaiigkigvaggtgyvvefagea 207
                                               a+a+gigtsevehv+atqt +  r+ t++i+v+g+   g++akd++l +i  ig+ag tgy ve+ag a
  lcl|FitnessBrowser__azobra:AZOBR_RS27815 141 AMAWGIGTSEVEHVMATQTAILRRPPTMRITVSGTRPAGVSAKDMVLKLIATIGTAGATGYGVEYAGPA 209
                                               ********************************************************************* PP

                                 TIGR00170 208 irdlsmeermtvcnmaieagakagliapdettfeyvkdrkyapkgkefekavaywktlktdegakfdkv 276
                                               ir+lsmeermtvcnm++e+ga+ gliapde+tf+y+++r++ap g+ +e+av  w++l +d+ga+fd +
  lcl|FitnessBrowser__azobra:AZOBR_RS27815 210 IRALSMEERMTVCNMSVELGARFGLIAPDEVTFAYLQGRPFAPAGALWEQAVVAWRALASDPGARFDAE 278
                                               ********************************************************************* PP

                                 TIGR00170 277 vtleakdispqvtwgtnpgqvlsvneevpdpksladpvekasaekalaylglepgtklkdikvdkvfig 345
                                               + l+ + ++pqv+wgt+p++ + v e+vpdp+  adp +++ + +al+y+glepgt+++d+ vd vfig
  lcl|FitnessBrowser__azobra:AZOBR_RS27815 279 IELDVSSLTPQVSWGTSPQDCIGVGETVPDPEREADPKRRQAMRRALDYIGLEPGTPIRDLPVDMVFIG 347
                                               ********************************************************************* PP

                                 TIGR00170 346 sctnsriedlraaaevvkgkkvadnvklalvvpgsglvkkqaekegldkifleagfewreagcslclgm 414
                                               sctnsriedlraaa+v+kg++va +++ alvvpgsg+v++qae+egld++f +agfewre+gcs+c gm
  lcl|FitnessBrowser__azobra:AZOBR_RS27815 348 SCTNSRIEDLRAAAAVLKGRRVAAGLR-ALVVPGSGQVRRQAEAEGLDRVFTAAGFEWREPGCSMCAGM 415
                                               ***************************.***************************************** PP

                                 TIGR00170 415 nndvldeyercastsnrnfegrqgkgarthlvspamaaaaavagkfvdire 465
                                               n d++++++rc +tsnrnfegrqg garthl spa aaaaavag++vd+r 
  lcl|FitnessBrowser__azobra:AZOBR_RS27815 416 NADRVPPGKRCVATSNRNFEGRQGPGARTHLASPATAAAAAVAGRIVDVRS 466
                                               *************************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (466 nodes)
Target sequences:                          1  (471 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.01
# Mc/sec: 11.19
//
[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:

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