Alignments for a candidate for hisC in Beijerinckia indica ATCC 9039

GapMind for Amino acid biosynthesis

Alignments for a candidate for hisC in Beijerinckia indica ATCC 9039

Align histidinol-phosphate aminotransferase [EC:2.6.1.9] (characterized)
to candidate WP_012383319.1 BIND_RS01560 histidinol-phosphate aminotransferase

Query= reanno::azobra:AZOBR_RS20485
         (364 letters)



>NCBI__GCF_000019845.1:WP_012383319.1
          Length = 378

 Score =  383 bits (984), Expect = e-111
 Identities = 192/359 (53%), Positives = 246/359 (68%), Gaps = 9/359 (2%)

Query: 8   PAPRPGILDIAPYVGGEHAGH-----IRLASNEGALGPSPRAVEAYRAAAGELHRYPDGG 62
           P P  G+L I PYV G+ A        +L+SNE  LGPSP A +A+ A+A +L  YPDG 
Sbjct: 15  PMPHAGVLGIEPYVPGKSAAPGVAKIHKLSSNETPLGPSPEAQKAFAASAEKLALYPDGA 74

Query: 63  SAKLRKAIAERFGLDADRVVCGAGSDELIALLIRAYAGPGDEVLYSQHGFLMYPIGAKSV 122
           +  LR AIA R GLD  R+VCGAGSDEL++LL   Y GPG+E ++++HGFL+Y I   + 
Sbjct: 75  ATLLRTAIASRHGLDPARIVCGAGSDELLSLLAAVYLGPGEEGIFTEHGFLVYKIAILTA 134

Query: 123 GATPVQAPETNLTTDVDSLLAHVTPRTRLVFVANPNNPTGTYITADEMARLHAGLPENAI 182
           G TP+  PE +LTTDVD++LA VTPRTR+V++ANPNNPTGTY+   E+ RL   LP N +
Sbjct: 135 GGTPIVVPEKDLTTDVDAILAAVTPRTRIVYIANPNNPTGTYLPFAEVKRLATSLPPNVL 194

Query: 183 LVIDAAYAEYMNHNDYSAGQELVDRFPNVVMTRTFSKIFALGSVRLGWAYCPAGIADVLN 242
           LV+DAAY EY+  NDYSAG ELV    NVVMTRTFSKI+ L ++RLGW Y P  +AD LN
Sbjct: 195 LVLDAAYGEYVTRNDYSAGLELVSTHENVVMTRTFSKIYGLAALRLGWCYAPLAVADALN 254

Query: 243 RVRGPFNVSSAAQIAGVAALEDTAFLERSRSHNIEWREWFVQQVHGLGLKTHPSVTNFVL 302
           RVRGPFN S  A   GVAAL D A ++R+ +HN  W  W  +++  LG K  PSV NF+L
Sbjct: 255 RVRGPFNTSGPAIATGVAALADQAHIDRAIAHNETWLSWLGEEIGKLGFKVTPSVANFLL 314

Query: 303 VDFAGQTAGKDDAEAARLFLKGRGILVRQMPAYGLPSCLRVTIGTEAEMREVVQALKDF 361
           + F  Q     +A+A   FL  RG+++R + +YGLP+CLR+T+GTE   R VV  LKDF
Sbjct: 315 LHFEDQA----EAQAVDAFLSSRGLILRAVASYGLPNCLRLTVGTEEANRLVVDGLKDF 369


Lambda     K      H
   0.319    0.136    0.405 

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: 427
Number of extensions: 13
Number of successful extensions: 3
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: 364
Length of database: 378
Length adjustment: 30
Effective length of query: 334
Effective length of database: 348
Effective search space:   116232
Effective search space used:   116232
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_012383319.1 BIND_RS01560 (histidinol-phosphate aminotransferase)
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.31725.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
      2e-87  279.3   0.0    2.2e-87  279.1   0.0    1.0  1  lcl|NCBI__GCF_000019845.1:WP_012383319.1  BIND_RS01560 histidinol-phosphat


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000019845.1:WP_012383319.1  BIND_RS01560 histidinol-phosphate aminotransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  279.1   0.0   2.2e-87   2.2e-87       4     347 ..      21     367 ..      18     369 .. 0.95

  Alignments for each domain:
  == domain 1  score: 279.1 bits;  conditional E-value: 2.2e-87
                                 TIGR01141   4 ikklepYqpgarelgek.evvkLnsnEnPfgpsekvkealkeelkklhrYpdpqalelkealakylgve 71 
                                               +  +epY+pg+++ ++  ++ kL+snE P+gps+++++a+ ++++kl +Ypd  a+ l++a+a++ g++
  lcl|NCBI__GCF_000019845.1:WP_012383319.1  21 VLGIEPYVPGKSAAPGVaKIHKLSSNETPLGPSPEAQKAFAASAEKLALYPDGAATLLRTAIASRHGLD 89 
                                               56789*****88888886888************************************************ PP

                                 TIGR01141  72 eenillgnGsdelielliraflepgdavlvleptysmYevsakiagaevkevplkedgqedleavleaa 140
                                               ++ i+ g+Gsdel++ll+  +l pg++ +++e+ + +Y++   +ag   + vp k+  + d++a+l+a+
  lcl|NCBI__GCF_000019845.1:WP_012383319.1  90 PARIVCGAGSDELLSLLAAVYLGPGEEGIFTEHGFLVYKIAILTAGGTPIVVPEKDL-TTDVDAILAAV 157
                                               *********************************************999999998777.69********* PP

                                 TIGR01141 141 kekvklvflasPnnPtGnllkreeiekvleev.edalVVvDeAYieFsee...asvlellaeypnlvvl 205
                                               + ++++v++a+PnnPtG++l  +e+++++ +   ++l V+D AY+e+ ++      lel++ ++n+v++
  lcl|NCBI__GCF_000019845.1:WP_012383319.1 158 TPRTRIVYIANPNNPTGTYLPFAEVKRLATSLpPNVLLVLDAAYGEYVTRndySAGLELVSTHENVVMT 226
                                               ********************************66**************998877789************ PP

                                 TIGR01141 206 rTlSKafgLAglRvGyaianaeiiealekvrapynvsslaleaavaalrdsdkiektveevkkererll 274
                                               rT+SK++gLA+lR+G  +a  ++++al++vr p+n+s +a +++vaal d+++i + +++++    +l 
  lcl|NCBI__GCF_000019845.1:WP_012383319.1 227 RTFSKIYGLAALRLGWCYAPLAVADALNRVRGPFNTSGPAIATGVAALADQAHIDRAIAHNETWLSWLG 295
                                               ********************************************************************* PP

                                 TIGR01141 275 eelkkleglevyeSkaNFvlikvke..daeelleallekgiivRdlksaeglleeclRitvGtreener 341
                                               ee+ kl g++v +S aNF+l++++   +a+++   l  +g+i+R ++s+ gl ++clR+tvGt+e n+ 
  lcl|NCBI__GCF_000019845.1:WP_012383319.1 296 EEIGKL-GFKVTPSVANFLLLHFEDqaEAQAVDAFLSSRGLILRAVASY-GL-PNCLRLTVGTEEANRL 361
                                               ******.8***************9875666666778899**********.85.**************99 PP

                                 TIGR01141 342 llealk 347
                                               +++ lk
  lcl|NCBI__GCF_000019845.1:WP_012383319.1 362 VVDGLK 367
                                               998776 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (349 nodes)
Target sequences:                          1  (378 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 8.89
//
[ok]

This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 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 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 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