GapMind for Amino acid biosynthesis

 

Alignments for a candidate for trpA in Sulfurihydrogenibium azorense Az-Fu1

Align tryptophan synthase subunit α (EC 4.1.2.8) (characterized)
to candidate WP_012674352.1 SULAZ_RS01860 tryptophan synthase subunit alpha

Query= metacyc::MONOMER-3561
         (251 letters)



>NCBI__GCF_000021545.1:WP_012674352.1
          Length = 255

 Score =  179 bits (455), Expect = 4e-50
 Identities = 100/241 (41%), Positives = 149/241 (61%), Gaps = 6/241 (2%)

Query: 7   LIPYLTAGDPSVEKTLEFLLA-VEEFAGLIELGIPFSDPMADGKTIQESHYRALRNGFKL 65
           LI Y  AG PSVE +++     +E  A ++E+G PFSDP+ADG TIQ +H +A+++G   
Sbjct: 12  LICYFMAGYPSVEDSIKTAFTLIENGADILEVGFPFSDPVADGVTIQVAHEKAVKDGITP 71

Query: 66  DDTFRILREFR-RHSSTPVILMTYYNPVFRTGVKKFLGEAKASGADGILVVDLPVSHAGE 124
           +  F+I +  + ++ + P+I MTYYNP+FR G + F   AK SG DG +V DLP    G 
Sbjct: 72  EKVFQITKTIKEKYPNVPLIGMTYYNPIFRFGEENFCNRAKESGIDGFIVPDLPPEEGGN 131

Query: 125 FLDAAKEEGLKTVFLAAPNTPDERLREIDKASTGFVYLISLYGTTGARDRLP-ETAFEFV 183
               A  +GL  +FL AP + +ER++ + K S  F+Y +SL G TG RD LP +   E +
Sbjct: 132 LKKVANRKGLSLIFLLAPTSNEERIKLVSKMSDDFIYYVSLTGITGERDTLPWDELKEKI 191

Query: 184 RRARKICNNKLAVGFGVSRREQVEELLKAGADGVVVGSALIELISRSENPVEELRRKVAE 243
              RKI + K+AVGFGVS+ E   +++   ADGV+VGS++++L  + +   E L+  V E
Sbjct: 192 TLIRKITDKKIAVGFGVSKGEHA-KIISQIADGVIVGSSVVKL--QGKRDFEGLKNLVKE 248

Query: 244 L 244
           L
Sbjct: 249 L 249


Lambda     K      H
   0.319    0.138    0.386 

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: 186
Number of extensions: 13
Number of successful extensions: 4
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: 251
Length of database: 255
Length adjustment: 24
Effective length of query: 227
Effective length of database: 231
Effective search space:    52437
Effective search space used:    52437
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: 46 (22.3 bits)

Align candidate WP_012674352.1 SULAZ_RS01860 (tryptophan synthase subunit alpha)
to HMM TIGR00262 (trpA: tryptophan synthase, alpha subunit (EC 4.2.1.20))

# 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/TIGR00262.hmm
# target sequence database:        /tmp/gapView.1269988.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00262  [M=256]
Accession:   TIGR00262
Description: trpA: tryptophan synthase, alpha subunit
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
    1.2e-81  259.4   0.1    1.5e-81  259.0   0.1    1.0  1  NCBI__GCF_000021545.1:WP_012674352.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000021545.1:WP_012674352.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  259.0   0.1   1.5e-81   1.5e-81       9     237 ..       9     237 ..       4     254 .. 0.94

  Alignments for each domain:
  == domain 1  score: 259.0 bits;  conditional E-value: 1.5e-81
                             TIGR00262   9 ekafvpFvtagdPdleksleiiktlvkaGadalElGvpfsDPlaDGptiqaaelRAlkagvkvekalellkkv 81 
                                            k ++ ++ ag+P++e s++ + tl+++Gad+lE+G+pfsDP+aDG tiq a+ +A+k+g+++ek+++++k +
  NCBI__GCF_000021545.1:WP_012674352.1   9 RKPLICYFMAGYPSVEDSIKTAFTLIENGADILEVGFPFSDPVADGVTIQVAHEKAVKDGITPEKVFQITKTI 81 
                                           5779********************************************************************* PP

                             TIGR00262  82 rekasniPivlltyynlifkkgveeFyakakeagvdgvlvaDlPleeaddlleaakkhgvkqiflvaPtaeee 154
                                           +ek++n+P++ +tyyn+if+ g+e+F ++ake+g+dg +v+DlP ee ++l ++a+++g++ ifl aPt++ee
  NCBI__GCF_000021545.1:WP_012674352.1  82 KEKYPNVPLIGMTYYNPIFRFGEENFCNRAKESGIDGFIVPDLPPEEGGNLKKVANRKGLSLIFLLAPTSNEE 154
                                           ************************************************************************* PP

                             TIGR00262 155 rlkkiaekseGfvYlvsvaGvtgarerve.eevkelikkvkalskkPvlvGFGiskkeqvkelkelgadgviv 226
                                           r+k +++ s+ f+Y vs +G+tg+r+ +  +e+ke i  ++++++k ++vGFG+sk e++k + ++ adgviv
  NCBI__GCF_000021545.1:WP_012674352.1 155 RIKLVSKMSDDFIYYVSLTGITGERDTLPwDELKEKITLIRKITDKKIAVGFGVSKGEHAKIISQI-ADGVIV 226
                                           ***************************973569****************************99999.9***** PP

                             TIGR00262 227 GsAlvkiieek 237
                                           Gs +vk+  ++
  NCBI__GCF_000021545.1:WP_012674352.1 227 GSSVVKLQGKR 237
                                           *****975544 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (256 nodes)
Target sequences:                          1  (255 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: 00:00:00.00
# Mc/sec: 20.94
//
[ok]

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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