GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hisC in Sphingomonas indica Dd16

Align Histidinol-phosphate aminotransferase; EC 2.6.1.9; Imidazole acetol-phosphate transaminase (uncharacterized)
to candidate WP_085217034.1 B9N75_RS00545 histidinol-phosphate transaminase

Query= curated2:P58891
         (363 letters)



>NCBI__GCF_900177405.1:WP_085217034.1
          Length = 549

 Score =  212 bits (540), Expect = 2e-59
 Identities = 141/334 (42%), Positives = 191/334 (57%), Gaps = 12/334 (3%)

Query: 27  ALQGD-VWLNANESAWA--NPADPDASTRRYPDPQPKGLRSALAALYGCAPEQLLIGRGS 83
           A+ GD + L+ANE+ +    PA   AS  RYP+PQP  L++ LA+LYG  P+ L++ RG+
Sbjct: 25  AVPGDTIKLDANENPFEPLGPAALAASVNRYPEPQPARLKAMLASLYGVDPDALVVTRGA 84

Query: 84  DEAIDLLVRGLCVPERDAVLVTPPVFGMYAVCARLQNAPLVDVPLVDGPDGFHADIPAIV 143
           D+AID+L+R  C P  DA+L+ PP F  YA  ARLQ A +V+  L  GPD F  D    V
Sbjct: 85  DDAIDMLIRAFCRPGDDAILIAPPTFTAYAHFARLQGARVVEHYL--GPD-FALDAQGFV 141

Query: 144 AMALSS-NAKLVFLCSPSNPAGSAIALDQIEQALQALQGKALVVVDEAYGEFSDVPSAVG 202
           A A ++ + KL FLCSP NP G  +A D +     AL  + ++VVDEAY EFS   S   
Sbjct: 142 AAARATPSLKLAFLCSPDNPTGGIVAADTLCAIADALP-ETILVVDEAYIEFSCAESVAR 200

Query: 203 LLGRYDNLAVLRTLSKAHALAAARIGTLIANAELIALLRRCQAPYPVPTPCAAMAEQALS 262
              R  NL VLRTLSKA  LA ARIG  I +  LIAL  R   PYP+ +   A A  AL+
Sbjct: 201 EAVRRPNLVVLRTLSKAFGLAGARIGAAIGSRALIALAARALPPYPLSSLSIAAALDALA 260

Query: 263 APALEVTRRRIAEVRSERERMHKALVQLPGVRQVYPSQGNFLLVRFDDAEGAFQALLEAG 322
                +   RIA + +ER RM + L +  G+ +V    GNFL +   D     ++   AG
Sbjct: 261 PERRRLHADRIARIIAERARMAERLRRASGLDRVRDGGGNFLFLEAKDPAKLRESFAAAG 320

Query: 323 VVVR-DQRAVPRLADALRITLGTNEQNQRVLSAL 355
           ++ R  + A P     +R+T+GT  +N  VL+AL
Sbjct: 321 ILARFRETAAP---GGVRLTIGTRAENDAVLAAL 351


Lambda     K      H
   0.319    0.133    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: 530
Number of extensions: 35
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: 363
Length of database: 549
Length adjustment: 32
Effective length of query: 331
Effective length of database: 517
Effective search space:   171127
Effective search space used:   171127
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: 51 (24.3 bits)

Align candidate WP_085217034.1 B9N75_RS00545 (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.1268802.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
      7e-91  290.6   0.0    8.8e-91  290.3   0.0    1.1  1  NCBI__GCF_900177405.1:WP_085217034.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_900177405.1:WP_085217034.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  290.3   0.0   8.8e-91   8.8e-91       2     346 ..      11     351 ..      10     353 .. 0.94

  Alignments for each domain:
  == domain 1  score: 290.3 bits;  conditional E-value: 8.8e-91
                             TIGR01141   2 ekikklepYqpgarelgekevvkLnsnEnPfgpsekvkealkeelkklhrYpdpqalelkealakylgveeen 74 
                                           ++i +l  ++++ r+++++ ++kL++nEnPf+p      a+ ++  +++rYp+pq+++lk++la+ +gv+++ 
  NCBI__GCF_900177405.1:WP_085217034.1  11 PEIVALGDFDIPPRAVPGD-TIKLDANENPFEPLG---PAALAA--SVNRYPEPQPARLKAMLASLYGVDPDA 77 
                                           6677777777777888885.9************95...444444..7************************** PP

                             TIGR01141  75 illgnGsdelielliraflepg.davlvleptysmYevsakiagaevkevplkedgqedleavle..aakekv 144
                                           +++++G+d++i++liraf+ pg da+l+++pt++ Y++ a+++ga+v+e  l  d+  d + + +   a+ + 
  NCBI__GCF_900177405.1:WP_085217034.1  78 LVVTRGADDAIDMLIRAFCRPGdDAILIAPPTFTAYAHFARLQGARVVEHYLGPDFALDAQGFVAaaRATPSL 150
                                           **********************99*******************************999999988744667788 PP

                             TIGR01141 145 klvflasPnnPtGnllkreeiekvleevedalVVvDeAYieFseeasvlellaeypnlvvlrTlSKafgLAgl 217
                                           kl fl+sP+nPtG ++ ++ +++++++  +++ VvDeAYieFs  +sv+  + ++pnlvvlrTlSKafgLAg 
  NCBI__GCF_900177405.1:WP_085217034.1 151 KLAFLCSPDNPTGGIVAADTLCAIADALPETILVVDEAYIEFSCAESVAREAVRRPNLVVLRTLSKAFGLAGA 223
                                           9**************************989******************************************* PP

                             TIGR01141 218 RvGyaianaeiiealekvrapynvsslaleaavaalrdsd..kiektveevkkererlleelkklegle.vye 287
                                           R+G ai++ ++i   ++  +py++ssl+ +aa+ al  ++    +++++++++er+r+ e l+  +gl+ v +
  NCBI__GCF_900177405.1:WP_085217034.1 224 RIGAAIGSRALIALAARALPPYPLSSLSIAAALDALAPERrrLHADRIARIIAERARMAERLRRASGLDrVRD 296
                                           ************************************9998878899***********************9*** PP

                             TIGR01141 288 SkaNFvlikvkedaeelleallekgiivRdlksaeglleeclRitvGtreenerlleal 346
                                           + +NF+++++k d ++l e+   +gi+ R  ++a    ++ +R+t+Gtr en+++l+al
  NCBI__GCF_900177405.1:WP_085217034.1 297 GGGNFLFLEAK-DPAKLRESFAAAGILARFRETA---APGGVRLTIGTRAENDAVLAAL 351
                                           *********99.999****************966...599****************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (349 nodes)
Target sequences:                          1  (549 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: 00:00:00.00
# Mc/sec: 20.81
//
[ok]

This GapMind analysis is from Jul 26 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