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.1115.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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 10.50
//
[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:

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:

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:

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:

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