Alignments for a candidate for hisC in Arcobacter nitrofigilis DSM 7299

GapMind for Amino acid biosynthesis

Alignments for a candidate for hisC in Arcobacter nitrofigilis DSM 7299

Align Histidinol-phosphate aminotransferase; EC 2.6.1.9; Imidazole acetol-phosphate transaminase (uncharacterized)
to candidate WP_013134239.1 ARNIT_RS02155 histidinol-phosphate transaminase

Query= curated2:Q7M7Y6
         (367 letters)



>NCBI__GCF_000092245.1:WP_013134239.1
          Length = 368

 Score =  456 bits (1173), Expect = e-133
 Identities = 222/366 (60%), Positives = 286/366 (78%)

Query: 1   MQFNPTLDSIKTYEAGKPIELVVREYGIKPQNVIKLASNENPFGASPKVIEAIAKEAVNA 60
           M+FN  L+++ TYEAGKPIELVVREYG+ P++VIKLASNENP+G S KV   I + A N 
Sbjct: 1   MKFNEVLENVTTYEAGKPIELVVREYGVNPKDVIKLASNENPYGTSSKVTAKIQELAKNM 60

Query: 61  HRYPDDSMFELKEGLAGRFGVKSENVIIGSGSDQILEMAVHAKCNASSKVLMSKTTFAMY 120
             YPDDSM+ELKE L  +F V S NVIIGSGSDQI+E  VHAKC   SK+LM+KTTFAMY
Sbjct: 61  FVYPDDSMYELKEALGKKFDVDSSNVIIGSGSDQIIEFCVHAKCEKDSKLLMAKTTFAMY 120

Query: 121 DVYSRQVGARILRTPSDQHHLGEFWEIYQKERPEILFLCLPNNPLGECLDREEVYDFLQK 180
           ++Y +Q GA+I++T S  H L +F  +Y++   +++FLCLPNNPLGE +D ++VY+FL++
Sbjct: 121 EIYGKQTGAKIIKTESHTHDLAQFLALYKEHGADVIFLCLPNNPLGEAVDTKDVYEFLEQ 180

Query: 181 IDDETLVIVDGAYQEYAAFKDSQKRIDPKDLIERFPSSIFLGTFSKAFGLGGMRVGYGIA 240
           ID ETLV+VDGAYQEYAA+KD  KRI PKDLI +F + I+LGTFSKA+ LGGMRVGYGIA
Sbjct: 181 IDSETLVVVDGAYQEYAAYKDENKRIVPKDLITKFSNCIYLGTFSKAYALGGMRVGYGIA 240

Query: 241 QPSIIQALMKMRAPFNITTLSLKAAIEALKESAYVEETIKENFKEMRRYEEFALAQGIDF 300
           QP II+ L K+RAPFNITTL+L AAIEALK+  +V   I +NF+EM RYEE+A ++G ++
Sbjct: 241 QPEIIKTLYKLRAPFNITTLTLAAAIEALKDEEFVTACIAKNFEEMTRYEEYAKSRGFEY 300

Query: 301 IPSYTNFITLLLKNRVDSSEFSQWLLERGLIVRNLKSYGINAIRITIGRSLENDRCFELM 360
           IPSYTNFIT+ + ++  S E +Q LLE G+IVR+L  YG NAIRITIG + +N + F ++
Sbjct: 301 IPSYTNFITIKMGDKFVSKEVAQKLLEVGIIVRDLTGYGQNAIRITIGTNEQNTKVFSVL 360

Query: 361 QEYLHQ 366
            E L +
Sbjct: 361 DEVLEK 366


Lambda     K      H
   0.320    0.137    0.392 

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: 452
Number of extensions: 17
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: 367
Length of database: 368
Length adjustment: 30
Effective length of query: 337
Effective length of database: 338
Effective search space:   113906
Effective search space used:   113906
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 WP_013134239.1 ARNIT_RS02155 (histidinol-phosphate transaminase)
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.4774.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.5e-105  338.2   2.4   2.8e-105  338.0   2.4    1.0  1  lcl|NCBI__GCF_000092245.1:WP_013134239.1  ARNIT_RS02155 histidinol-phospha


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000092245.1:WP_013134239.1  ARNIT_RS02155 histidinol-phosphate transaminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  338.0   2.4  2.8e-105  2.8e-105       2     349 .]       5     363 ..       4     363 .. 0.95

  Alignments for each domain:
  == domain 1  score: 338.0 bits;  conditional E-value: 2.8e-105
                                 TIGR01141   2 ekikklepYqpg......arelgek..evvkLnsnEnPfgpsekvkealkeelkklhrYpdpqalelke 62 
                                               e +++++ Y++g       re+g +  +v+kL+snEnP+g+s kv+++++e +k++  Ypd++++elke
  lcl|NCBI__GCF_000092245.1:WP_013134239.1   5 EVLENVTTYEAGkpielvVREYGVNpkDVIKLASNENPYGTSSKVTAKIQELAKNMFVYPDDSMYELKE 73 
                                               5688999********999999999999****************************************** PP

                                 TIGR01141  63 alakylgveeenillgnGsdelielliraflepgdavlvleptysmYevsakiagaevkevplkedgqe 131
                                               al k+++v+  n+++g Gsd++ie+ ++a +e+  + l+++ t++mYe++ k++ga++++++ +++   
  lcl|NCBI__GCF_000092245.1:WP_013134239.1  74 ALGKKFDVDSSNVIIGSGSDQIIEFCVHAKCEKDSKLLMAKTTFAMYEIYGKQTGAKIIKTESHTHDLA 142
                                               ************************************************************999998544 PP

                                 TIGR01141 132 dleavleaakekvklvflasPnnPtGnllkreeiekvleev.edalVVvDeAYieFsee......asvl 193
                                               ++ a+   +++ ++++fl+ PnnP G+ ++++++ ++le+  +++lVVvD AY e++            
  lcl|NCBI__GCF_000092245.1:WP_013134239.1 143 QFLAL--YKEHGADVIFLCLPNNPLGEAVDTKDVYEFLEQIdSETLVVVDGAYQEYAAYkdenkrIVPK 209
                                               44444..5999******************************66*************9887777666677 PP

                                 TIGR01141 194 ellaeypnlvvlrTlSKafgLAglRvGyaianaeiiealekvrapynvsslaleaavaalrdsdkiekt 262
                                               +l+++++n ++l T+SKa++L+g+RvGy+ia++eii++l k+rap+n+++l+l+aa++al+d++++ ++
  lcl|NCBI__GCF_000092245.1:WP_013134239.1 210 DLITKFSNCIYLGTFSKAYALGGMRVGYGIAQPEIIKTLYKLRAPFNITTLTLAAAIEALKDEEFVTAC 278
                                               99******************************************************************* PP

                                 TIGR01141 263 veevkkererlleelkkleglevyeSkaNFvlikvke..daeelleallekgiivRdlksaeglleecl 329
                                               ++++ +e++r++e +k   g+e+++S++NF++ik+     ++e++++lle giivRdl+ + g  ++++
  lcl|NCBI__GCF_000092245.1:WP_013134239.1 279 IAKNFEEMTRYEEYAKSR-GFEYIPSYTNFITIKMGDkfVSKEVAQKLLEVGIIVRDLTGY-G--QNAI 343
                                               ***********9999988.8***************988889******************88.5..7*** PP

                                 TIGR01141 330 RitvGtreenerllealkei 349
                                               Rit+Gt+e+n++++ +l+e+
  lcl|NCBI__GCF_000092245.1:WP_013134239.1 344 RITIGTNEQNTKVFSVLDEV 363
                                               ****************9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (349 nodes)
Target sequences:                          1  (368 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: 7.19
//
[ok]

This GapMind analysis is from Apr 10 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