Alignments for a candidate for hcs in Herbaspirillum seropedicae SmR1

GapMind for Amino acid biosynthesis

Alignments for a candidate for hcs in Herbaspirillum seropedicae SmR1

Align Homocitrate synthase; EC 2.3.3.14 (characterized)
to candidate HSERO_RS14210 HSERO_RS14210 homocitrate synthase

Query= SwissProt::P05342
         (385 letters)



>FitnessBrowser__HerbieS:HSERO_RS14210
          Length = 376

 Score =  426 bits (1094), Expect = e-124
 Identities = 216/365 (59%), Positives = 279/365 (76%), Gaps = 1/365 (0%)

Query: 4   VIIDDTTLRDGEQSAGVAFNADEKIAIARALAELGVPELEIGIPSMGEEEREVMHAIAGL 63
           V I+DTTLRDGEQ+AGVAF A+EKI IARAL E+GVPE+EIGIP MG+ E EV+ AIA L
Sbjct: 2   VTINDTTLRDGEQTAGVAFTAEEKIDIARALDEIGVPEMEIGIPIMGQAEIEVIQAIAAL 61

Query: 64  GLSSRLLAWCRLCDVDLAAARSTGVTMVDLSLPVSDLMLHHKLNRDRDWALREVARLVGE 123
            L S+ + W R+C+ DLAAA      +V+LS+PVSD+ + HKL RDRDW L ++   + +
Sbjct: 62  PLRSKTMVWGRMCEADLAAAARCNADIVNLSMPVSDIHIQHKLQRDRDWVLAQIRHFLPK 121

Query: 124 ARMAGLEVCLGCEDASRADLEFVVQVGEVAQAAGARRLRFADTVGVMEPFGMLDRFRFLS 183
           A   G+EVCLG ED+SRADL+F+++V E AQAAGARR RFADT+G+++PF   +  R L 
Sbjct: 122 ALDLGMEVCLGGEDSSRADLDFMLRVIETAQAAGARRFRFADTLGLLDPFATYEVIRQLR 181

Query: 184 RRLDMELEVHAHDDFGLATANTLAAVMGGATHINTTVNGLGERAGNAALEECVLALKNLH 243
           + +D+ELE+HAH+D GLATANTLAA+  GA+H+NTTVNGLGERAGNA LEE V+ L++LH
Sbjct: 182 QEVDIELEMHAHNDLGLATANTLAAINAGASHVNTTVNGLGERAGNAPLEEVVMGLRHLH 241

Query: 244 GIDTGIDTRGIPAISALVERASGRQVAWQKSVVGAGVFTHEAGIHVDGLLKHRRNYEGLN 303
           GI+T +DTR +PAIS LV +ASG+ VA  KS+VG  VFTHE+GIHVDGLLK+  NYE  +
Sbjct: 242 GIETQVDTRSLPAISRLVAKASGKAVAPNKSIVGEAVFTHESGIHVDGLLKNPANYEHFS 301

Query: 304 PDELGRSHSLVLGKHSGAHMVRNTYRDLGIELADWQSQALLGRIRAFSTRTKRRSPQPAE 363
           P ELGRSH +VLGKHSG+  V++ +  +GI L+D Q+QA+L RIR   T   + +P   E
Sbjct: 302 PAELGRSHHIVLGKHSGSRGVKDAFAKMGILLSDSQAQAMLMRIRD-HTMVAKAAPSEDE 360

Query: 364 LQDFY 368
           L  F+
Sbjct: 361 LTRFF 365


Lambda     K      H
   0.320    0.135    0.396 

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: 442
Number of extensions: 11
Number of successful extensions: 1
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: 385
Length of database: 376
Length adjustment: 30
Effective length of query: 355
Effective length of database: 346
Effective search space:   122830
Effective search space used:   122830
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: 50 (23.9 bits)

Align candidate HSERO_RS14210 HSERO_RS14210 (homocitrate synthase)
to HMM TIGR02660 (nifV: homocitrate synthase (EC 2.3.3.14))

# 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/TIGR02660.hmm
# target sequence database:        /tmp/gapView.19546.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR02660  [M=365]
Accession:   TIGR02660
Description: nifV_homocitr: homocitrate synthase
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-165  536.6   4.2     2e-165  536.4   4.2    1.0  1  lcl|FitnessBrowser__HerbieS:HSERO_RS14210  HSERO_RS14210 homocitrate syntha


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__HerbieS:HSERO_RS14210  HSERO_RS14210 homocitrate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  536.4   4.2    2e-165    2e-165       2     364 ..       2     364 ..       1     365 [. 0.99

  Alignments for each domain:
  == domain 1  score: 536.4 bits;  conditional E-value: 2e-165
                                  TIGR02660   2 vlinDttLRDGEqaagvaFsaeEKlaiAkaLdeaGvdelEvGipamgeeEraairaiaalglkarlla 69 
                                                v+inDttLRDGEq+agvaF+aeEK+ iA+aLde+Gv+e+E+Gip mg++E+++i+aiaal l++++++
  lcl|FitnessBrowser__HerbieS:HSERO_RS14210   2 VTINDTTLRDGEQTAGVAFTAEEKIDIARALDEIGVPEMEIGIPIMGQAEIEVIQAIAALPLRSKTMV 69 
                                                89****************************************************************** PP

                                  TIGR02660  70 WcRlraedieaaaevGvkavdlsvpvsdlqleaklkkdrawvleelkelvslakeeglkvsvgaeDas 137
                                                W R++++d++aaa++  + v+ls+pvsd+++++kl++dr+wvl+++++++ +a + g++v++g+eD+s
  lcl|FitnessBrowser__HerbieS:HSERO_RS14210  70 WGRMCEADLAAAARCNADIVNLSMPVSDIHIQHKLQRDRDWVLAQIRHFLPKALDLGMEVCLGGEDSS 137
                                                ******************************************************************** PP

                                  TIGR02660 138 RadeeflvelaevakeagakRlRfaDtvgvldPfstyelvkalraalelelElHaHnDlGlAtAntla 205
                                                Rad +f+ +++e+a++aga+R+RfaDt+g+ldPf+tye +++lr+++++elE+HaHnDlGlAtAntla
  lcl|FitnessBrowser__HerbieS:HSERO_RS14210 138 RADLDFMLRVIETAQAAGARRFRFADTLGLLDPFATYEVIRQLRQEVDIELEMHAHNDLGLATANTLA 205
                                                ******************************************************************** PP

                                  TIGR02660 206 avkaGassvsvtvlGlGERAGnAaleevalalkellgldtgidlselkelsqlvakasgraleaqkav 273
                                                a++aGas+v++tv+GlGERAGnA+leev+++l++l+g++t++d+++l+++s+lvakasg+a++++k++
  lcl|FitnessBrowser__HerbieS:HSERO_RS14210 206 AINAGASHVNTTVNGLGERAGNAPLEEVVMGLRHLHGIETQVDTRSLPAISRLVAKASGKAVAPNKSI 273
                                                ******************************************************************** PP

                                  TIGR02660 274 vGesvFaHEsGiHvdgllkdeatYesldPeevGrerelviGKHsgraaviealkelgleleeeeaeel 341
                                                vGe+vF+HEsGiHvdgllk++a+Ye+++P+e+Gr++++v+GKHsg+++v++a++++g+ l++++a+++
  lcl|FitnessBrowser__HerbieS:HSERO_RS14210 274 VGEAVFTHESGIHVDGLLKNPANYEHFSPAELGRSHHIVLGKHSGSRGVKDAFAKMGILLSDSQAQAM 341
                                                ******************************************************************** PP

                                  TIGR02660 342 leavravaerlKrsleeeelaal 364
                                                l ++r+++  +K +++e+el+++
  lcl|FitnessBrowser__HerbieS:HSERO_RS14210 342 LMRIRDHTMVAKAAPSEDELTRF 364
                                                ********************876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (365 nodes)
Target sequences:                          1  (376 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: 00:00:00.01
# Mc/sec: 7.79
//
[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