Alignments for a candidate for hisC in Sinorhizobium meliloti 1021

GapMind for Amino acid biosynthesis

Alignments for a candidate for hisC in Sinorhizobium meliloti 1021

Align histidinol-phosphate aminotransferase (EC 2.6.1.9) (characterized)
to candidate SMc03885 SMc03885 histidinol-phosphate aminotransferase

Query= reanno::Marino:GFF2483
         (350 letters)



>FitnessBrowser__Smeli:SMc03885
          Length = 351

 Score =  419 bits (1078), Expect = e-122
 Identities = 210/350 (60%), Positives = 263/350 (75%)

Query: 1   MSKFWSPLVNDLVPYVPGEQPKMANLVKLNTNENPFGPSPKVIEAIQAELNDGLRLYPDP 60
           MSK WSP+V  L PYVPGEQP+MA+LVKLNTNE+P+GPS K + AI+A  +  LRLYPDP
Sbjct: 1   MSKLWSPIVAALKPYVPGEQPRMADLVKLNTNESPYGPSEKALGAIRAAADTDLRLYPDP 60

Query: 61  EGESLRETIAAYHKITPEQIFLGNGSDEVLAHIFFGLFQHGEPILFPDITYSFYPVYCGL 120
               LR+ IAA H+++  ++F+GNGSDEVLAH F  L +H  P+LFPDI+YSFY  Y GL
Sbjct: 61  VALGLRQAIAARHQVSVGEVFVGNGSDEVLAHTFAALLKHDRPLLFPDISYSFYTTYAGL 120

Query: 121 YNIESKKVPLTESFEINPEDFKQPNGGVIFPNPNAPTGRYLELQYVEEILAANPNRVVVV 180
           + IE+ +VPL  +F I+  D+++P+G VI PNPNAPTG  L L  +E ++A +P + VV+
Sbjct: 121 FGIEAVEVPLDAAFRIDIADYRRPSGAVILPNPNAPTGIGLPLAEIERLVADHPGQPVVI 180

Query: 181 DEAYIDFGGESAITLVDKYPNLLVSQTLSKARSLAGLRVGFAVGHPDLIEALNRVKNSFN 240
           DEAYIDFGGESAI LV KY NLLV QT SK+R+LAGLRVGFA+G   LIEAL RVK+SFN
Sbjct: 181 DEAYIDFGGESAIALVPKYDNLLVVQTFSKSRALAGLRVGFAIGQRPLIEALERVKDSFN 240

Query: 241 SYPLDRLALAGAKAAYEDEAWFRKCCDGVISERERVTAVLEGLGFEVLPSKANFIFARHK 300
           SYPL R A AGA AA EDEAWF      +I+ R ++T+ LE  GFEVLPS+ANF+FARH 
Sbjct: 241 SYPLGRAAQAGATAAIEDEAWFEATRGKIIASRAKLTSELEKRGFEVLPSQANFVFARHP 300

Query: 301 EQPGEVLAKGLREQGIIVRHFNKPRISEFLRITIGTVEQNDALIARLESL 350
              G+ LA  LRE+ +IVRHF KPRI++FLRITIGT  +   L+A L+ +
Sbjct: 301 GHAGQTLAAKLRERAVIVRHFAKPRIADFLRITIGTDAECAKLVAALDEV 350


Lambda     K      H
   0.319    0.139    0.410 

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: 388
Number of extensions: 10
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: 350
Length of database: 351
Length adjustment: 29
Effective length of query: 321
Effective length of database: 322
Effective search space:   103362
Effective search space used:   103362
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 (21.7 bits)
S2: 49 (23.5 bits)

Align candidate SMc03885 SMc03885 (histidinol-phosphate aminotransferase)
to HMM TIGR01141 (hisC: histidinol-phosphate transaminase (EC 2.6.1.9))

# 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/TIGR01141.hmm
# target sequence database:        /tmp/gapView.2566.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01141  [M=349]
Accession:   TIGR01141
Description: hisC: histidinol-phosphate transaminase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
      4e-89  284.9   0.0    4.5e-89  284.7   0.0    1.0  1  lcl|FitnessBrowser__Smeli:SMc03885  SMc03885 histidinol-phosphate am


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Smeli:SMc03885  SMc03885 histidinol-phosphate aminotransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  284.7   0.0   4.5e-89   4.5e-89       4     349 .]       9     350 ..       6     350 .. 0.94

  Alignments for each domain:
  == domain 1  score: 284.7 bits;  conditional E-value: 4.5e-89
                           TIGR01141   4 ikklepYqpgarelgekevvkLnsnEnPfgpsekvkealkeelk.klhrYpdpqalelkealakylgveeenill 77 
                                         + +l+pY+pg++     + vkLn+nE+P+gpsek++ a++++++ +l++Ypdp al l++a+a++ +v++ ++++
  lcl|FitnessBrowser__Smeli:SMc03885   9 VAALKPYVPGEQPRMA-DLVKLNTNESPYGPSEKALGAIRAAADtDLRLYPDPVALGLRQAIAARHQVSVGEVFV 82 
                                         7799*****9777666.5************************999****************************** PP

                           TIGR01141  78 gnGsdelielliraflepgdavlvleptysmYevsakiagaevkevplkedgqedleavleaakekvklvflasP 152
                                         gnGsde++   + a+l+  +  l+++ +ys Y ++a + g+e +evpl++ ++ d ++      +    v l +P
  lcl|FitnessBrowser__Smeli:SMc03885  83 GNGSDEVLAHTFAALLKHDRPLLFPDISYSFYTTYAGLFGIEAVEVPLDAAFRIDIADYR----RPSGAVILPNP 153
                                         ***************************************************977777777....5566789**** PP

                           TIGR01141 153 nnPtGnllkreeiekvleevedalVVvDeAYieFseeasvlellaeypnlvvlrTlSKafgLAglRvGyaianae 227
                                         n+PtG  l  +eie++++      VV+DeAYi+F +e s++ l+ +y+nl+v++T+SK+ +LAglRvG+ai++  
  lcl|FitnessBrowser__Smeli:SMc03885 154 NAPTGIGLPLAEIERLVADHPGQPVVIDEAYIDFGGE-SAIALVPKYDNLLVVQTFSKSRALAGLRVGFAIGQRP 227
                                         *******************87899************7.************************************* PP

                           TIGR01141 228 iiealekvrapyn...vsslaleaavaalrdsdkiektveevkkererlleelkkleglevyeSkaNFvlikvke 299
                                         +ieale+v++++n   + + a++ a+aa++d++ +e+t  +++++r+ l++el+k  g+ev +S+aNFv+++ + 
  lcl|FitnessBrowser__Smeli:SMc03885 228 LIEALERVKDSFNsypLGRAAQAGATAAIEDEAWFEATRGKIIASRAKLTSELEKR-GFEVLPSQANFVFARHPG 301
                                         *********98653337889999********************************9.8****************9 PP

                           TIGR01141 300 .daeelleallekgiivRdlksaeglleeclRitvGtreenerllealkei 349
                                          + + l+ +l e+ +ivR++++    + ++lRit+Gt+ e+ +l++al+e+
  lcl|FitnessBrowser__Smeli:SMc03885 302 hAGQTLAAKLRERAVIVRHFAKP--RIADFLRITIGTDAECAKLVAALDEV 350
                                         778889999***********954..68*********************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (349 nodes)
Target sequences:                          1  (351 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01
# Mc/sec: 12.08
//
[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