GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hisC in Thioalkalivibrio thiocyanodenitrificans ARhD 1

Align Histidinol-phosphate aminotransferase; EC 2.6.1.9 (characterized, see rationale)
to candidate WP_018232412.1 THITHI_RS0107235 histidinol-phosphate transaminase

Query= uniprot:A0A2R7PAQ8
         (373 letters)



>NCBI__GCF_000378965.1:WP_018232412.1
          Length = 363

 Score =  291 bits (744), Expect = 3e-83
 Identities = 166/357 (46%), Positives = 226/357 (63%), Gaps = 14/357 (3%)

Query: 15  IRPDVRAMHSYVVQPSTGMLKMDAMENPFRLPAHLQAALGQRLGSVALNRYPGDRIADLK 74
           IRP +RA+ +Y V  +TG++K+DAMENP+  P  L  A  + L  VALNRYP  R   L 
Sbjct: 13  IRPGIRALAAYHVPDATGLVKLDAMENPYHWPRELVDAWLEVLRGVALNRYPDPRSPQLI 72

Query: 75  AALAQYAGMPEGYGIVLGNGSDELITLLALACAQPGTGQRATMLAPMPGFVMYPLSAQLQ 134
             L + AG+P    ++LGNGSDELI ++ +A A+PG      +++  P FVMY +     
Sbjct: 73  DTLRRVAGIPAEQSVILGNGSDELIQVIIMALAEPGR----VVMSVEPSFVMYRMITGYA 128

Query: 135 GLDFVGVPLTPDFELDEPAMLAAIGQHRPAITYIAYPNNPTATLWDEGAVQRIIDAAGAQ 194
            +++VGVPL  DF LD PA LAA+  HRPA+ ++AYPNNPT   +    V+ +I AA   
Sbjct: 129 DMNYVGVPLGEDFALDTPAFLAAMKAHRPAVVFLAYPNNPTGNRFSRPDVEAVIRAAP-- 186

Query: 195 GGIVVMDEAYQPFASRTWIDRMRAEPARNAHVLLMRTLSKFGLAGVRLGYLIGPSAFVSE 254
            G+VV+DEAY PFA     D   ++  R  ++++MRT+SK GLAG+RLGYL GP+A++SE
Sbjct: 187 -GLVVLDEAYAPFAD----DSFLSDLGRYPNLVVMRTVSKQGLAGLRLGYLCGPAAWLSE 241

Query: 255 IDKVRPPYNVSVLNCEAALFALEHAEVFAAQAAEIRVERATLIAALRQMPGVEKCWDSEA 314
            DKVR PYN++VL   +A FAL H  V   QAA IR +R TL  AL  +PGV   + SEA
Sbjct: 242 FDKVRLPYNINVLTQASADFALAHHHVLDEQAAAIRRDRETLARALAGLPGVTP-YPSEA 300

Query: 315 NMVLIRV--ADSAKAYEGMKNRKVLVKNVSTMHPLLANCLRLTVGNAEDNAQMLAAL 369
           N +L RV        ++G+K   VL+KN+S     L +CLR+TVG  E+N + LAAL
Sbjct: 301 NFILFRVPAGRGDAVFQGLKEAGVLIKNLSGQGGALTDCLRVTVGRPEENERFLAAL 357


Lambda     K      H
   0.321    0.134    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: 411
Number of extensions: 21
Number of successful extensions: 5
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: 373
Length of database: 363
Length adjustment: 30
Effective length of query: 343
Effective length of database: 333
Effective search space:   114219
Effective search space used:   114219
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 (21.9 bits)
S2: 49 (23.5 bits)

Align candidate WP_018232412.1 THITHI_RS0107235 (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.304672.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   6.8e-103  330.1   0.0   7.7e-103  330.0   0.0    1.0  1  NCBI__GCF_000378965.1:WP_018232412.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000378965.1:WP_018232412.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  330.0   0.0  7.7e-103  7.7e-103       1     348 [.      14     359 ..      14     360 .. 0.96

  Alignments for each domain:
  == domain 1  score: 330.0 bits;  conditional E-value: 7.7e-103
                             TIGR01141   1 rekikklepYqpgarelgekevvkLnsnEnPfgpsekvkealkeelk..klhrYpdpqalelkealakylgve 71 
                                           r+ i++l++Y+ +   +  ++ vkL+++EnP+  ++++++a+ e l+   l+rYpdp + +l  +l++++g+ 
  NCBI__GCF_000378965.1:WP_018232412.1  14 RPGIRALAAYHVP---D-ATGLVKLDAMENPYHWPRELVDAWLEVLRgvALNRYPDPRSPQLIDTLRRVAGIP 82 
                                           6789999999994...2.2368*************************999*********************76 PP

                             TIGR01141  72 een.illgnGsdelielliraflepgdavlvleptysmYevsakiagaevkevplkedgqedleavle.aake 142
                                           +e+ ++lgnGsdeli+++i+a++epg+ v+ +ep++ mY++++  a+++++ vpl ed+  d++a+l+  +++
  NCBI__GCF_000378965.1:WP_018232412.1  83 AEQsVILGNGSDELIQVIIMALAEPGRVVMSVEPSFVMYRMITGYADMNYVGVPLGEDFALDTPAFLAaMKAH 155
                                           6554*************************************************************99978999 PP

                             TIGR01141 143 kvklvflasPnnPtGnllkreeiekvleevedalVVvDeAYieFseeasvlellaeypnlvvlrTlSKafgLA 215
                                           ++ +vfla+PnnPtGn ++r ++e+v+ ++  +lVV+DeAY  F+++ s+l+ l +ypnlvv+rT+SK   LA
  NCBI__GCF_000378965.1:WP_018232412.1 156 RPAVVFLAYPNNPTGNRFSRPDVEAVIRAA-PGLVVLDEAYAPFADD-SFLSDLGRYPNLVVMRTVSKQG-LA 225
                                           *****************************8.9**************8.********************87.** PP

                             TIGR01141 216 glRvGyaianaeiiealekvrapynvsslaleaavaalrdsdkiektveevkkererlleelkkleglevyeS 288
                                           glR+Gy+ + a++ ++++kvr pyn+++l+++ a  al +++ + ++ ++++++re l  +l+ l+g+  y+S
  NCBI__GCF_000378965.1:WP_018232412.1 226 GLRLGYLCGPAAWLSEFDKVRLPYNINVLTQASADFALAHHHVLDEQAAAIRRDRETLARALAGLPGVTPYPS 298
                                           ************************************************************************* PP

                             TIGR01141 289 kaNFvlikvke.daeelleallekgiivRdlksaeglleeclRitvGtreenerllealke 348
                                           +aNF+l++v++   +++++ l+e+g+++++l+ + g l++clR+tvG +eener+l+al +
  NCBI__GCF_000378965.1:WP_018232412.1 299 EANFILFRVPAgRGDAVFQGLKEAGVLIKNLSGQGGALTDCLRVTVGRPEENERFLAALGR 359
                                           **********999*********************************************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (349 nodes)
Target sequences:                          1  (363 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 0.01s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 14.77
//
[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