Alignments for a candidate for hisC in Cupriavidus basilensis 4G11

GapMind for Amino acid biosynthesis

Alignments for a candidate for hisC in Cupriavidus basilensis 4G11

Align Histidinol-phosphate aminotransferase; EC 2.6.1.9 (characterized, see rationale)
to candidate RR42_RS18910 RR42_RS18910 histidinol-phosphate aminotransferase

Query= uniprot:A0A2R7PAQ8
         (373 letters)



>FitnessBrowser__Cup4G11:RR42_RS18910
          Length = 366

 Score =  376 bits (965), Expect = e-109
 Identities = 200/361 (55%), Positives = 259/361 (71%), Gaps = 11/361 (3%)

Query: 15  IRPDVRAMHSYVVQPSTGMLKMDAMENPFRLPAHLQAALGQRLGSVALNRYPGDRIADLK 74
           IR DVRAM +Y V  S G++K+DAMENP++LP  L+A L  RL  VALNRYP      L+
Sbjct: 13  IRDDVRAMGAYHVPDSHGLVKLDAMENPYQLPDALRAKLAARLAEVALNRYPVPSSEVLR 72

Query: 75  AALAQYAGMPEGYGIVLGNGSDELITLLALACAQPGTGQRATMLAPMPGFVMYPLSAQLQ 134
           A L     +P G  ++LGNGSDE+I++L+LA A+PG    A +LAP+PGFVMY +SAQ  
Sbjct: 73  ARLKTVMDVPAGMDVLLGNGSDEIISMLSLAAAKPG----AKVLAPVPGFVMYAMSAQFA 128

Query: 135 GLDFVGVPLTPDFELDEPAMLAAIGQHRPAITYIAYPNNPTATLWDEGAVQRIIDAAGAQ 194
           GL+FVGVPL  DF LD  AMLAA+ +H+PAI Y+AYPNNPT  L+D   ++ I+ AA  +
Sbjct: 129 GLEFVGVPLKADFTLDRAAMLAAMAEHQPAIIYLAYPNNPTGNLFDADDMEAIVRAAQGE 188

Query: 195 G--GIVVMDEAYQPFASRTWIDRMRAEPARNAHVLLMRTLSKFGLAGVRLGYLIGPSAFV 252
               +VV+DEAYQPFA  TW+ R+    A   ++L+MRT+SK GLAG+RLGYL G  A++
Sbjct: 189 TCQSLVVVDEAYQPFAQDTWMPRL----AEFGNLLVMRTVSKLGLAGIRLGYLAGAPAWL 244

Query: 253 SEIDKVRPPYNVSVLNCEAALFALEHAEVFAAQAAEIRVERATLIAALRQMPGVEKCWDS 312
           S+IDKVRPPYNV+VL    ALF LEH +V   QAA++R ERAT+ +AL  +PGV   + S
Sbjct: 245 SQIDKVRPPYNVNVLTEATALFVLEHVDVLDQQAAQLRAERATVASALAALPGV-TVYPS 303

Query: 313 EANMVLIRVADSAKAYEGMKNRKVLVKNVSTMHPLLANCLRLTVGNAEDNAQMLAALQAS 372
            AN +L+RV DSA+ ++G+  RKVL+KNV  MHPLLANCLR+TV   E+NAQ L A QA+
Sbjct: 304 AANFLLVRVDDSARVFDGVLARKVLIKNVGKMHPLLANCLRVTVSTPEENAQFLVAFQAA 363

Query: 373 L 373
           L
Sbjct: 364 L 364


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: 395
Number of extensions: 19
Number of successful extensions: 6
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: 366
Length adjustment: 30
Effective length of query: 343
Effective length of database: 336
Effective search space:   115248
Effective search space used:   115248
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 RR42_RS18910 RR42_RS18910 (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.23066.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
    4.3e-97  311.0   0.0    4.9e-97  310.9   0.0    1.0  1  lcl|FitnessBrowser__Cup4G11:RR42_RS18910  RR42_RS18910 histidinol-phosphat


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cup4G11:RR42_RS18910  RR42_RS18910 histidinol-phosphate aminotransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  310.9   0.0   4.9e-97   4.9e-97       1     347 [.      14     361 ..      14     363 .. 0.95

  Alignments for each domain:
  == domain 1  score: 310.9 bits;  conditional E-value: 4.9e-97
                                 TIGR01141   1 rekikklepYqpgarelgek.evvkLnsnEnPfgpsekvkealkeelk..klhrYpdpqalelkealak 66 
                                               r++++++ +Y+ +     ++ + vkL+++EnP++ +++++++l ++l+   l+rYp p++  l+++l  
  lcl|FitnessBrowser__Cup4G11:RR42_RS18910  14 RDDVRAMGAYHVP-----DShGLVKLDAMENPYQLPDALRAKLAARLAevALNRYPVPSSEVLRARLKT 77 
                                               6788999999984.....33378************************98999***************** PP

                                 TIGR01141  67 ylgvee.enillgnGsdelielliraflepgdavlvleptysmYevsakiagaevkevplkedgqedle 134
                                               +++v +  ++llgnGsde+i++l  a ++pg++vl++ p + mY++sa++ag e + vplk+d++ d +
  lcl|FitnessBrowser__Cup4G11:RR42_RS18910  78 VMDVPAgMDVLLGNGSDEIISMLSLAAAKPGAKVLAPVPGFVMYAMSAQFAGLEFVGVPLKADFTLDRA 146
                                               ***765279******************************************************999999 PP

                                 TIGR01141 135 avle.aakekvklvflasPnnPtGnllkreeiekvleev..e..dalVVvDeAYieFseeasvlellae 198
                                               a+l+  a++++ +++la+PnnPtGnl++++++e+++ ++  e  + lVVvDeAY  F+++ ++++ lae
  lcl|FitnessBrowser__Cup4G11:RR42_RS18910 147 AMLAaMAEHQPAIIYLAYPNNPTGNLFDADDMEAIVRAAqgEtcQSLVVVDEAYQPFAQD-TWMPRLAE 214
                                               988868999**************************99886435678*************8.******** PP

                                 TIGR01141 199 ypnlvvlrTlSKafgLAglRvGyaianaeiiealekvrapynvsslaleaavaalrdsdkiektveevk 267
                                               + nl+v+rT+SK+  LAg+R+Gy+ + +++ ++++kvr+pynv++l+ ++a+  l++ d + ++ ++++
  lcl|FitnessBrowser__Cup4G11:RR42_RS18910 215 FGNLLVMRTVSKLG-LAGIRLGYLAGAPAWLSQIDKVRPPYNVNVLTEATALFVLEHVDVLDQQAAQLR 282
                                               ************86.****************************************************** PP

                                 TIGR01141 268 kererlleelkkleglevyeSkaNFvlikvkedaeelleallekgiivRdlksaeglleeclRitvGtr 336
                                               +er+ + ++l++l+g+ vy+S aNF+l++v+ d++++++ +l +++++++++++++ll +clR+tv t+
  lcl|FitnessBrowser__Cup4G11:RR42_RS18910 283 AERATVASALAALPGVTVYPSAANFLLVRVD-DSARVFDGVLARKVLIKNVGKMHPLLANCLRVTVSTP 350
                                               ******************************9.************************************* PP

                                 TIGR01141 337 eenerllealk 347
                                               een ++l a++
  lcl|FitnessBrowser__Cup4G11:RR42_RS18910 351 EENAQFLVAFQ 361
                                               *******9886 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (349 nodes)
Target sequences:                          1  (366 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: 7.76
//
[ok]

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

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