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 3; EC 2.6.1.9; Imidazole acetol-phosphate transaminase 3 (uncharacterized)
to candidate SMa0387 SMa0387 histidinol-phosphate aminotransferase

Query= curated2:Q930J0
         (370 letters)



>FitnessBrowser__Smeli:SMa0387
          Length = 370

 Score =  732 bits (1889), Expect = 0.0
 Identities = 370/370 (100%), Positives = 370/370 (100%)

Query: 1   MAIPSRPIREEIRSIAPYNAGLTLEEVRAKYHVDEVAKLSSNENPLGPSPALRRLFPDIG 60
           MAIPSRPIREEIRSIAPYNAGLTLEEVRAKYHVDEVAKLSSNENPLGPSPALRRLFPDIG
Sbjct: 1   MAIPSRPIREEIRSIAPYNAGLTLEEVRAKYHVDEVAKLSSNENPLGPSPALRRLFPDIG 60

Query: 61  ELARLYPDPQGRALCARLAASFDVENNQVILGNGSEDLIAVICRSVVRAGDTVVTLYPSF 120
           ELARLYPDPQGRALCARLAASFDVENNQVILGNGSEDLIAVICRSVVRAGDTVVTLYPSF
Sbjct: 61  ELARLYPDPQGRALCARLAASFDVENNQVILGNGSEDLIAVICRSVVRAGDTVVTLYPSF 120

Query: 121 PLHEDYTTLMGGKVDRVTVTPDLSVDMDALLAAIARKPRMLMFSNPMNPVGSWLTPLQLA 180
           PLHEDYTTLMGGKVDRVTVTPDLSVDMDALLAAIARKPRMLMFSNPMNPVGSWLTPLQLA
Sbjct: 121 PLHEDYTTLMGGKVDRVTVTPDLSVDMDALLAAIARKPRMLMFSNPMNPVGSWLTPLQLA 180

Query: 181 KVVAALDPETLIVVDEAYAEYAAGDDYPSAAEVLKVTGLNWVVLRTFSKAYGLAGLRIGY 240
           KVVAALDPETLIVVDEAYAEYAAGDDYPSAAEVLKVTGLNWVVLRTFSKAYGLAGLRIGY
Sbjct: 181 KVVAALDPETLIVVDEAYAEYAAGDDYPSAAEVLKVTGLNWVVLRTFSKAYGLAGLRIGY 240

Query: 241 GIVSDGSLCDFFNRARTPFNTNAIAQVSALAAFDDTYHLNRSVELALVERERMKKELATM 300
           GIVSDGSLCDFFNRARTPFNTNAIAQVSALAAFDDTYHLNRSVELALVERERMKKELATM
Sbjct: 241 GIVSDGSLCDFFNRARTPFNTNAIAQVSALAAFDDTYHLNRSVELALVERERMKKELATM 300

Query: 301 GYRIAPSKCNFLFFDARTEATPVAEALLRRGVIVKPWKQPRFETYIRVSIGSPVENDHFI 360
           GYRIAPSKCNFLFFDARTEATPVAEALLRRGVIVKPWKQPRFETYIRVSIGSPVENDHFI
Sbjct: 301 GYRIAPSKCNFLFFDARTEATPVAEALLRRGVIVKPWKQPRFETYIRVSIGSPVENDHFI 360

Query: 361 HALKEVEAVG 370
           HALKEVEAVG
Sbjct: 361 HALKEVEAVG 370


Lambda     K      H
   0.320    0.136    0.398 

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: 576
Number of extensions: 5
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: 370
Length of database: 370
Length adjustment: 30
Effective length of query: 340
Effective length of database: 340
Effective search space:   115600
Effective search space used:   115600
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: 49 (23.5 bits)

Align candidate SMa0387 SMa0387 (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.31559.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                          -----------
    2.9e-91  291.9   0.0    3.2e-91  291.7   0.0    1.0  1  lcl|FitnessBrowser__Smeli:SMa0387  SMa0387 histidinol-phosphate ami


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Smeli:SMa0387  SMa0387 histidinol-phosphate aminotransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  291.7   0.0   3.2e-91   3.2e-91       1     349 []       9     366 ..       9     366 .. 0.94

  Alignments for each domain:
  == domain 1  score: 291.7 bits;  conditional E-value: 3.2e-91
                          TIGR01141   1 rekikklepYqpg......arelgekevvkLnsnEnPfgpsekvkealkeelk.klhrYpdpqalelkealakylg 69 
                                        re+i++++pY++g        ++  +ev kL+snEnP+gps+++  +l   +    ++Ypdpq+ +l ++la+ ++
  lcl|FitnessBrowser__Smeli:SMa0387   9 REEIRSIAPYNAGltleevRAKYHVDEVAKLSSNENPLGPSPAL-RRLFPDIGeLARLYPDPQGRALCARLAASFD 83 
                                        799************999766777779**************955.5566666625567****************** PP

                          TIGR01141  70 veeenillgnGsdelielliraflepgdavlvleptysmYevsakiagaevkevplkedgqedleavleaakekvk 145
                                        ve+++++lgnGs++li +++r+++  gd+v++l p++ ++e ++++ g +v  v ++ d + d++a+l+a+++k++
  lcl|FitnessBrowser__Smeli:SMa0387  84 VENNQVILGNGSEDLIAVICRSVVRAGDTVVTLYPSFPLHEDYTTLMGGKVDRVTVTPDLSVDMDALLAAIARKPR 159
                                        ***********************************************************99*************** PP

                          TIGR01141 146 lvflasPnnPtGnllkreeiekvleeve.dalVVvDeAYieFsee...asvlellaeyp.nlvvlrTlSKafgLAg 216
                                        +  + +P nP+G++l+  ++ kv+++   ++l+VvDeAY e++     +s++e+l+    n vvlrT+SKa+gLAg
  lcl|FitnessBrowser__Smeli:SMa0387 160 MLMFSNPMNPVGSWLTPLQLAKVVAALDpETLIVVDEAYAEYAAGddyPSAAEVLKVTGlNWVVLRTFSKAYGLAG 235
                                        ***************************66**************98788999999998888**************** PP

                          TIGR01141 217 lRvGyaian.aeiiealekvrapynvsslaleaavaalrdsdkiektveevkkererlleelkkleglevyeSkaN 291
                                        lR+Gy+i++  ++ + +++ r+p+n++ +a+  a+aa +d  +++++ve    erer+++el+++ g ++ +Sk N
  lcl|FitnessBrowser__Smeli:SMa0387 236 LRIGYGIVSdGSLCDFFNRARTPFNTNAIAQVSALAAFDDTYHLNRSVELALVERERMKKELATM-GYRIAPSKCN 310
                                        *****9875169*****************************************************.8********* PP

                          TIGR01141 292 FvlikvkedaeelleallekgiivRdlksaeglleeclRitvGtreenerllealkei 349
                                        F++++++++a+ ++eall++g+iv+  k+     e+++R+++G++ en+++++alke+
  lcl|FitnessBrowser__Smeli:SMa0387 311 FLFFDARTEATPVAEALLRRGVIVKPWKQP--RFETYIRVSIGSPVENDHFIHALKEV 366
                                        ***************************944..57*********************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (349 nodes)
Target sequences:                          1  (370 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: 12.02
//
[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