Alignments for a candidate for hisC in Stenotrophomonas chelatiphaga DSM 21508

GapMind for Amino acid biosynthesis

Alignments for a candidate for hisC in Stenotrophomonas chelatiphaga DSM 21508

Align Histidinol-phosphate aminotransferase; Imidazole acetol-phosphate transaminase; HPAT; HspAT; EC 2.6.1.9 (characterized)
to candidate WP_057506749.1 ABB28_RS00535 histidinol-phosphate transaminase

Query= SwissProt::P06986
         (356 letters)



>NCBI__GCF_001431535.1:WP_057506749.1
          Length = 364

 Score =  273 bits (698), Expect = 5e-78
 Identities = 150/357 (42%), Positives = 212/357 (59%), Gaps = 6/357 (1%)

Query: 2   STVTITDLARENVRNLTPYQSARRLGGNGDVWLNANEYPTAVEFQLTQQTLNRYPECQPK 61
           S   +  L R ++++   Y SAR     GDVWLNANE   A     +  +  RYP+ QP 
Sbjct: 4   SVQDVLALLRPDLQSFAGYSSARSTALQGDVWLNANESAWANPADASGSS-RRYPDPQPP 62

Query: 62  AVIENYAQYAGVKPEQVLVSRGADEGIELLIRAFCEPGKDAILYCPPTYGMYSVSAETIG 121
           A+++  A   GV P+Q+LV RG+DE I+LL+RAFC PG DA+L  PP +GMY+V A   G
Sbjct: 63  ALLQALAGLYGVSPQQLLVGRGSDEAIDLLVRAFCRPGVDAVLATPPVFGMYAVCARLQG 122

Query: 122 VECRTVPTLDN---WQLDLQGI--SDKLDGVKVVYVCSPNNPTGQLINPQDFRTLLELTR 176
                VP +D+    Q+DL  +  + +  G ++V++CSP+NP G  I+  D     +  +
Sbjct: 123 APLLEVPLVDSPAGLQVDLDAVIATARGQGARLVFLCSPSNPAGSEISAADIARTAQALQ 182

Query: 177 GKAIVVADEAYIEFCPQASLAGWLAEYPHLAILRTLSKAFALAGLRCGFTLANEEVINLL 236
           G+A+VV DEAYIE+  Q S    LA YP+LA+LRTLSKA ALA  R G  +A  E+I  L
Sbjct: 183 GQAVVVVDEAYIEYSGQPSATALLAHYPNLAVLRTLSKAHALAAARVGSLIAAPEIIAAL 242

Query: 237 MKVIAPYPLSTPVADIAAQALSPQGIVAMRERVAQIIAEREYLIAALKEIPCVEQVFDSE 296
            +  APYP+  P A++A  AL P  + A R R+  ++ ER  L  AL  +  V QV+ S 
Sbjct: 243 RRCQAPYPVPQPCAELAVAALQPAALAATRARIDDVVRERARLSDALAGVDGVRQVYPSA 302

Query: 297 TNYILARFKASSAVFKSLWDQGIILRDQNKQPSLSGCLRITVGTREESQRVIDALRA 353
            NY+L RF  +   F +L   G+++RDQ   P L   LRI++G+ +E+QRV+ AL A
Sbjct: 303 GNYLLVRFDDAQGAFDALLAAGVVVRDQRAAPQLGDALRISIGSTDENQRVLAALSA 359


Lambda     K      H
   0.319    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: 386
Number of extensions: 17
Number of successful extensions: 3
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: 356
Length of database: 364
Length adjustment: 29
Effective length of query: 327
Effective length of database: 335
Effective search space:   109545
Effective search space used:   109545
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_057506749.1 ABB28_RS00535 (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.29505.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   4.3e-110  353.8   0.0   4.9e-110  353.6   0.0    1.0  1  lcl|NCBI__GCF_001431535.1:WP_057506749.1  ABB28_RS00535 histidinol-phospha


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_001431535.1:WP_057506749.1  ABB28_RS00535 histidinol-phosphate transaminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  353.6   0.0  4.9e-110  4.9e-110       1     347 [.      13     358 ..      13     360 .. 0.96

  Alignments for each domain:
  == domain 1  score: 353.6 bits;  conditional E-value: 4.9e-110
                                 TIGR01141   1 rekikklepYqpgarelgekevvkLnsnEnPfgpsekvkealkeelkklhrYpdpqalelkealakylg 69 
                                               r+++++++ Y++ ar+++ +++v+Ln+nE++++++     +++    + +rYpdpq+ +l +ala  +g
  lcl|NCBI__GCF_001431535.1:WP_057506749.1  13 RPDLQSFAGYSS-ARSTALQGDVWLNANESAWANPA----DASG---SSRRYPDPQPPALLQALAGLYG 73 
                                               7899********.9*********************3....3333...369******************* PP

                                 TIGR01141  70 veeenillgnGsdelielliraflepg.davlvleptysmYevsakiagaevkevplked...gqedle 134
                                               v+++++l+g+Gsde+i+ll+raf+ pg davl+++p + mY+v+a+++ga + evpl ++    q dl+
  lcl|NCBI__GCF_001431535.1:WP_057506749.1  74 VSPQQLLVGRGSDEAIDLLVRAFCRPGvDAVLATPPVFGMYAVCARLQGAPLLEVPLVDSpagLQVDLD 142
                                               ***********************************************************9998666777 PP

                                 TIGR01141 135 avle.aakekvklvflasPnnPtGnllkreeiekvleeve.dalVVvDeAYieFseeasvlellaeypn 201
                                               av + a+ + ++lvfl+sP+nP G+ +++++i + +++ + +a+VVvDeAYie+s+++s++ lla+ypn
  lcl|NCBI__GCF_001431535.1:WP_057506749.1 143 AVIAtARGQGARLVFLCSPSNPAGSEISAADIARTAQALQgQAVVVVDEAYIEYSGQPSATALLAHYPN 211
                                               6665499999*****************************77**************************** PP

                                 TIGR01141 202 lvvlrTlSKafgLAglRvGyaianaeiiealekvrapynvsslaleaavaalrdsd..kiektveevkk 268
                                               l+vlrTlSKa++LA+ RvG +ia +eii al++++apy+v+++++e+avaal+ ++   +++++++v +
  lcl|NCBI__GCF_001431535.1:WP_057506749.1 212 LAVLRTLSKAHALAAARVGSLIAAPEIIAALRRCQAPYPVPQPCAELAVAALQPAAlaATRARIDDVVR 280
                                               *******************************************************999999******** PP

                                 TIGR01141 269 ererlleelkklegle.vyeSkaNFvlikvkedaeelleallekgiivRdlksaeglleeclRitvGtr 336
                                               er+rl ++l+ ++g++ vy+S +N++l++++ da+ +++all +g++vRd+++a++ l ++lRi++G+ 
  lcl|NCBI__GCF_001431535.1:WP_057506749.1 281 ERARLSDALAGVDGVRqVYPSAGNYLLVRFD-DAQGAFDALLAAGVVVRDQRAAPQ-LGDALRISIGST 347
                                               ******************************9.********************9976.6*********** PP

                                 TIGR01141 337 eenerllealk 347
                                               +en+r+l+al+
  lcl|NCBI__GCF_001431535.1:WP_057506749.1 348 DENQRVLAALS 358
                                               ********996 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (349 nodes)
Target sequences:                          1  (364 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: 10.18
//
[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