GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hisC in Thioalkalivibrio thiocyanodenitrificans ARhD 1

Align histidinol-phosphate aminotransferase; tyrosine/phenylalanine aminotransferase (promiscuous) (EC 2.6.1.1; EC 2.6.1.9) (characterized)
to candidate WP_018231479.1 THITHI_RS0102420 histidinol-phosphate transaminase

Query= metacyc::BSU22620-MONOMER
         (360 letters)



>NCBI__GCF_000378965.1:WP_018231479.1
          Length = 373

 Score =  291 bits (744), Expect = 2e-83
 Identities = 158/359 (44%), Positives = 218/359 (60%), Gaps = 5/359 (1%)

Query: 7   LKQLKPYQPGKPIEAVKSEYGLDKVVKLASNENPYGCSEAAKEALHHEIQQLALYPDGYS 66
           ++ L PYQPGKPI+ ++ E G+ + VKLASNENP G    A +A   ++  +ALYPDG  
Sbjct: 13  VQNLTPYQPGKPIDELERELGIRESVKLASNENPLGPGVRALDAARAQLSGVALYPDGNG 72

Query: 67  AALRTRLSKHLNVSETSLIFGNGSDEIIQIICRAFLNDKTNTVTAAPTFPQYKHNAVIEG 126
            AL+ RL+++LNV  T +  GNGS+EI+++I RAFL    N V +A  F  Y       G
Sbjct: 73  FALKRRLAEYLNVDATRITLGNGSNEILELIARAFLAPGRNAVFSAHAFAVYPIVVQAVG 132

Query: 127 AEVR-EIALRPDG----SHDLDAMLEAIDEQTQVVWICSPNNPTGTYTSEGELLAFLERV 181
           AE R  +A  PD      HDLDAM   ID  T+VV++ +PNNPTGT+  E  + AFL+RV
Sbjct: 133 AEARVAVANGPDHVLPWGHDLDAMAALIDGDTRVVFVANPNNPTGTWLDEASVHAFLKRV 192

Query: 182 PSRVLVVLDEAYYEYVTAEDYPETVPLLSKYSNLMILRTFSKAYGLAALRVGYGIADENL 241
           P   L V+DEAY+EY   + YP+    L  + NL++ RTFSK +GLA LR+GYG++ E +
Sbjct: 193 PEDTLAVMDEAYFEYAEVDGYPDATRWLDAFPNLIVTRTFSKIHGLAGLRIGYGVSGEAV 252

Query: 242 IRQIEPAREPFNTSRLGQAAAIAALDDQAFIASCVEQNNAGLQQYYDFAKTHGLKCYPSQ 301
              +   R+PFNT+ L QAAA+AALDD   +   V+ N  GL+Q        GL   PS 
Sbjct: 253 ADILNRVRQPFNTNSLAQAAALAALDDADHVRRSVQVNREGLRQLTAACGQRGLGFIPSV 312

Query: 302 TNFVLIDFKRPADELFQALLEKGYIVRSGNALGFPTSLRITIGTKEQNEEILAILAEIL 360
            NF+ ID  R A  +++ALL +G IVR     G P  LR+T+G + +N   +  L ++L
Sbjct: 313 GNFLSIDVGREAAPVYEALLRQGVIVRPIAGYGLPNHLRVTVGREHENRRFIDALDKVL 371


Lambda     K      H
   0.317    0.134    0.382 

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: 360
Number of extensions: 15
Number of successful extensions: 2
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: 360
Length of database: 373
Length adjustment: 30
Effective length of query: 330
Effective length of database: 343
Effective search space:   113190
Effective search space used:   113190
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 49 (23.5 bits)

Align candidate WP_018231479.1 THITHI_RS0102420 (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.281266.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   5.8e-111  356.7   0.0   6.5e-111  356.5   0.0    1.0  1  NCBI__GCF_000378965.1:WP_018231479.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000378965.1:WP_018231479.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  356.5   0.0  6.5e-111  6.5e-111       3     348 ..      12     369 ..      10     370 .. 0.98

  Alignments for each domain:
  == domain 1  score: 356.5 bits;  conditional E-value: 6.5e-111
                             TIGR01141   3 kikklepYqpg......arelgekevvkLnsnEnPfgpsekvkealkeelkklhrYpdpqalelkealakylg 69 
                                            +++l+pYqpg      +relg+ e vkL+snEnP+gp  ++++a++++l+ + +Ypd ++++lk++la+yl+
  NCBI__GCF_000378965.1:WP_018231479.1  12 GVQNLTPYQPGkpidelERELGIRESVKLASNENPLGPGVRALDAARAQLSGVALYPDGNGFALKRRLAEYLN 84 
                                           599********************************************************************** PP

                             TIGR01141  70 veeenillgnGsdelielliraflepgdavlvleptysmYevsakiagaevkevplked.....gqedleavl 137
                                           v+++ i+lgnGs+e++el++rafl pg++++++ +++++Y++++++ gae + + ++       + +dl+a++
  NCBI__GCF_000378965.1:WP_018231479.1  85 VDATRITLGNGSNEILELIARAFLAPGRNAVFSAHAFAVYPIVVQAVGAEARVAVANGPdhvlpWGHDLDAMA 157
                                           **************************************************9877666545899999******* PP

                             TIGR01141 138 eaakekvklvflasPnnPtGnllkreeiekvleev.edalVVvDeAYieFsee...asvlellaeypnlvvlr 206
                                           + ++ ++++vf+a+PnnPtG++l+++ + ++l++v ed+l+V+DeAY e++e    ++++ +l  +pnl+v+r
  NCBI__GCF_000378965.1:WP_018231479.1 158 ALIDGDTRVVFVANPNNPTGTWLDEASVHAFLKRVpEDTLAVMDEAYFEYAEVdgyPDATRWLDAFPNLIVTR 230
                                           ***********************************99***************99999**************** PP

                             TIGR01141 207 TlSKafgLAglRvGyaianaeiiealekvrapynvsslaleaavaalrdsdkiektveevkkererlleelkk 279
                                           T+SK++gLAglR+Gy+++ ++++++l++vr+p+n++sla++aa+aal+d+d+++++v+ ++++ ++l++++ +
  NCBI__GCF_000378965.1:WP_018231479.1 231 TFSKIHGLAGLRIGYGVSGEAVADILNRVRQPFNTNSLAQAAALAALDDADHVRRSVQVNREGLRQLTAACGQ 303
                                           ************************************************************************9 PP

                             TIGR01141 280 leglevyeSkaNFvlikvkedaeelleallekgiivRdlksaeglleeclRitvGtreenerllealke 348
                                             gl  ++S +NF+ i+v ++a+ ++eall++g+ivR ++ + gl +++lR+tvG ++en+r+++al++
  NCBI__GCF_000378965.1:WP_018231479.1 304 R-GLGFIPSVGNFLSIDVGREAAPVYEALLRQGVIVRPIAGY-GL-PNHLRVTVGREHENRRFIDALDK 369
                                           9.8***************************************.85.********************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (349 nodes)
Target sequences:                          1  (373 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: 17.41
//
[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