Alignments for a candidate for hisC in Flavobacterium glycines Gm-149

GapMind for Amino acid biosynthesis

Alignments for a candidate for hisC in Flavobacterium glycines Gm-149

Align histidinol-phosphate aminotransferase (EC 2.6.1.9) (characterized)
to candidate WP_066326077.1 BLR17_RS14015 histidinol-phosphate transaminase

Query= reanno::Btheta:349730
         (346 letters)



>NCBI__GCF_900100165.1:WP_066326077.1
          Length = 349

 Score =  357 bits (916), Expect = e-103
 Identities = 178/340 (52%), Positives = 238/340 (70%), Gaps = 2/340 (0%)

Query: 4   LQELTRPNIWKLKPYSSARDEYKG--AVASVFLDANENPYNLPHNRYPDPMQWELKTLLS 61
           +  L R N+  LKPYSSARDE++       VFLDANENPY    NRYPDP Q  +K  L 
Sbjct: 6   INTLIRENVKVLKPYSSARDEFEDFDTAEMVFLDANENPYQNGVNRYPDPQQANVKVALG 65

Query: 62  KIKKVSPQHIFLGNGSDEAIDLVFRAFCEPEKDNVVAIDPTYGMYQVCADVNNVEYRKVL 121
            IK ++PQ I LGNGSDE +DL+FRAFCEP+ DNV+ + PTYGMY V A++NNVE +++L
Sbjct: 66  AIKNLNPQQILLGNGSDEVLDLLFRAFCEPKVDNVITLPPTYGMYGVLANINNVENKEIL 125

Query: 122 LDENFQFSAEKLLAATDERTKLIFLCSPNNPTGNDLLRSEIEKILREFEGLVILDEAYND 181
           L  +FQ   +K+L A    TKLIFLCSPNNPTGN      +  +L +F G V++DEAY D
Sbjct: 126 LTNDFQPQVDKILEAVTPTTKLIFLCSPNNPTGNSFTTESVTTLLEKFNGFVVIDEAYID 185

Query: 182 FSEAPSFLEELDKYPNLVVFQTFSKAWGCAAIRLGMAFASEAIIGILSKIKYPYNVNQLT 241
           FS+  S+LE+LD+YPNL++ QT SKA+G A IRLG+ +AS  +I +L+KIK PYNVN+LT
Sbjct: 186 FSDKASWLEKLDQYPNLIITQTLSKAYGLAGIRLGICYASTEVIAVLNKIKPPYNVNELT 245

Query: 242 QQQAIAMLHKYYEIERWIKTLKEERDYLEEEFAKLSCTVRMYPSDSNFFLAKVTDAVKIY 301
           QQ+A+  L+   +I R I ++ EERD L +    +S   ++YP+++NF L KV DA K Y
Sbjct: 246 QQRALERLNDQEKINREISSILEERDTLLDVLNHVSFVEKIYPTEANFILIKVDDANKRY 305

Query: 302 NYLVGEGIIVRNRHSISLCCNCLRVTVGTRVENNTLLAAL 341
           + L+ +GI++RNR +  LC N LR+T+GT  EN  L+ AL
Sbjct: 306 DELIAKGIVIRNRTTQPLCENTLRLTIGTAEENKKLMKAL 345


Lambda     K      H
   0.320    0.136    0.402 

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: 399
Number of extensions: 19
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: 346
Length of database: 349
Length adjustment: 29
Effective length of query: 317
Effective length of database: 320
Effective search space:   101440
Effective search space used:   101440
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_066326077.1 BLR17_RS14015 (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.3546440.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   4.5e-113  363.6   0.7   7.4e-113  362.9   0.7    1.3  1  NCBI__GCF_900100165.1:WP_066326077.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_900100165.1:WP_066326077.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  362.9   0.7  7.4e-113  7.4e-113       1     348 [.      11     347 ..      11     348 .. 0.98

  Alignments for each domain:
  == domain 1  score: 362.9 bits;  conditional E-value: 7.4e-113
                             TIGR01141   1 rekikklepYqpgarelgek....evvkLnsnEnPfgpsekvkealkeelkklhrYpdpqalelkealakylg 69 
                                           re++k l+pY++ ar+ +e+    e+v L++nEnP+++              ++rYpdpq++++k al +  +
  NCBI__GCF_900100165.1:WP_066326077.1  11 RENVKVLKPYSS-ARDEFEDfdtaEMVFLDANENPYQNG-------------VNRYPDPQQANVKVALGAIKN 69 
                                           789*********.67777766779************987.............89******************* PP

                             TIGR01141  70 veeenillgnGsdelielliraflepg.davlvleptysmYevsakiagaevkevplkedgqedleavleaak 141
                                           +++++illgnGsde+++ll+raf+ep+ d+v++l+pty mY v a+i+++e ke+ l++d+q +++++lea++
  NCBI__GCF_900100165.1:WP_066326077.1  70 LNPQQILLGNGSDEVLDLLFRAFCEPKvDNVITLPPTYGMYGVLANINNVENKEILLTNDFQPQVDKILEAVT 142
                                           ************************************************************************* PP

                             TIGR01141 142 ekvklvflasPnnPtGnllkreeiekvleevedalVVvDeAYieFseeasvlellaeypnlvvlrTlSKafgL 214
                                             +kl+fl+sPnnPtGn++++e ++++le+  +++VV+DeAYi+Fs++as+le l +ypnl++++TlSKa+gL
  NCBI__GCF_900100165.1:WP_066326077.1 143 PTTKLIFLCSPNNPTGNSFTTESVTTLLEKF-NGFVVIDEAYIDFSDKASWLEKLDQYPNLIITQTLSKAYGL 214
                                           ******************************9.9**************************************** PP

                             TIGR01141 215 AglRvGyaianaeiiealekvrapynvsslaleaavaalrdsdkiektveevkkererlleelkklegle.vy 286
                                           Ag+R+G+ +a+ e+i +l+k+++pynv++l+++ a++ l+d++ki++ + ++ +er+ ll+ l++++ +e +y
  NCBI__GCF_900100165.1:WP_066326077.1 215 AGIRLGICYASTEVIAVLNKIKPPYNVNELTQQRALERLNDQEKINREISSILEERDTLLDVLNHVSFVEkIY 287
                                           *********************************************************************99** PP

                             TIGR01141 287 eSkaNFvlikvkedaeelleallekgiivRdlksaeglleeclRitvGtreenerllealke 348
                                           + +aNF+likv+ da++ +++l+ kgi++R+ +++ +l+e+ lR+t+Gt+een++l++al e
  NCBI__GCF_900100165.1:WP_066326077.1 288 PTEANFILIKVD-DANKRYDELIAKGIVIRNRTTQ-PLCENTLRLTIGTAEENKKLMKALTE 347
                                           ***********9.*******************977.79*********************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (349 nodes)
Target sequences:                          1  (349 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: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 6.45
//
[ok]

This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 2024.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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 2024 update 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 original 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