Alignments for a candidate for hisC in Chlorobium phaeobacteroides BS1

GapMind for Amino acid biosynthesis

Alignments for a candidate for hisC in Chlorobium phaeobacteroides BS1

Align Histidinol-phosphate aminotransferase; EC 2.6.1.9; Imidazole acetol-phosphate transaminase (uncharacterized)
to candidate WP_012474521.1 CPHAMN1_RS05465 histidinol-phosphate transaminase

Query= curated2:Q3ARM7
         (363 letters)



>NCBI__GCF_000020545.1:WP_012474521.1
          Length = 365

 Score =  421 bits (1082), Expect = e-122
 Identities = 212/343 (61%), Positives = 261/343 (76%)

Query: 10  LLNPALRNIATYKVEGGQQAEIKLNQNESPFDVPQWLKEEIIGEFIREPWNRYPDILPYR 69
           +LNPAL+ I  Y VEGGQ AEIKLNQNESPFD+P+ LK+ I+ EF +E WNRYPDILPYR
Sbjct: 18  MLNPALQRIGAYSVEGGQSAEIKLNQNESPFDLPEGLKDAILDEFKQESWNRYPDILPYR 77

Query: 70  AMEAYANFVGVPAECVIMSNGSNEMLYTIFLACLGPGRKVLIPNPSFSLYEKLALLLQSD 129
            ++AYA F GV  E V+MSNGSNEMLYTIF+ACL  G ++++P PSFSLY+KLA++LQ++
Sbjct: 78  GIQAYAEFTGVSPESVMMSNGSNEMLYTIFIACLEKGSRIVLPEPSFSLYDKLAIMLQAE 137

Query: 130 IVEVPMKSDLSFDVEAIMKAAHNEAVDVIVLSNPNNPTSTSMSYDAVRKIAESTQALVLV 189
            + VPM  DL FDV  I++ A  E    IVLS PNNPT  S+S + +R I     A+VLV
Sbjct: 138 RIIVPMHDDLGFDVPEIIRRAQEERAAFIVLSTPNNPTGKSLSIEDIRMIVHEVDAIVLV 197

Query: 190 DEAYIEFSRERSMVDTIEELPNVVVLRTMSKALALAGIRIGFALANAPLMAEISKPKIPF 249
           DEAY+EFSRE S +  I+E PN++VLRTMSKALALAG+RIGFAL N  L+AEI+KPKIPF
Sbjct: 198 DEAYVEFSREDSALCLIDEAPNLIVLRTMSKALALAGMRIGFALTNPALLAEIAKPKIPF 257

Query: 250 ASSRLAEITLMKVLANYRLVDEAVSAILSERDALYEQLRMMEGVSPFASDTNFLIVRVAD 309
            SSRLAEITL  VLANY LV+E+VS IL ER+ +YE L+ + G+  F SD NF+I+RV +
Sbjct: 258 TSSRLAEITLQHVLANYHLVEESVSYILQERERIYEALKGISGLHVFESDANFIIIRVRN 317

Query: 310 ANATFKRLYDKGILVRNVSGYHLMEGCLRCNVGLPEENRRLAE 352
           A   F  L  +GILVRNVSGY LM+ CLR N+GL +EN  L E
Sbjct: 318 AQEVFSFLAGEGILVRNVSGYPLMQNCLRFNIGLRKENDLLLE 360


Lambda     K      H
   0.319    0.134    0.378 

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: 409
Number of extensions: 11
Number of successful extensions: 1
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: 365
Length adjustment: 29
Effective length of query: 334
Effective length of database: 336
Effective search space:   112224
Effective search space used:   112224
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_012474521.1 CPHAMN1_RS05465 (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.27376.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
    1.9e-95  305.6   0.0    2.2e-95  305.4   0.0    1.0  1  lcl|NCBI__GCF_000020545.1:WP_012474521.1  CPHAMN1_RS05465 histidinol-phosp


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000020545.1:WP_012474521.1  CPHAMN1_RS05465 histidinol-phosphate transaminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  305.4   0.0   2.2e-95   2.2e-95       4     347 ..      23     363 ..      20     365 .] 0.96

  Alignments for each domain:
  == domain 1  score: 305.4 bits;  conditional E-value: 2.2e-95
                                 TIGR01141   4 ikklepYqpgarelgekevvkLnsnEnPfgpsekvkealkeelk..klhrYpdpqalelkealakylgv 70 
                                               ++ + +Y+    e g+++ +kLn nE+Pf+ +e +k+a+ +e k  + +rYpd  +++  +a+a+++gv
  lcl|NCBI__GCF_000020545.1:WP_012474521.1  23 LQRIGAYSV---EGGQSAEIKLNQNESPFDLPEGLKDAILDEFKqeSWNRYPDILPYRGIQAYAEFTGV 88 
                                               566667777...5677799**********************999889********************** PP

                                 TIGR01141  71 eeenillgnGsdelielliraflepgdavlvleptysmYevsakiagaevkevplked.gqedleavle 138
                                               ++e+++++nGs+e++ +++ a+le+g +++ +ep++s+Y   a + +ae + vp+++d g++  e +  
  lcl|NCBI__GCF_000020545.1:WP_012474521.1  89 SPESVMMSNGSNEMLYTIFIACLEKGSRIVLPEPSFSLYDKLAIMLQAERIIVPMHDDlGFDVPEIIRR 157
                                               **********************************************************76666666777 PP

                                 TIGR01141 139 aakekvklvflasPnnPtGnllkreeiekvleevedalVVvDeAYieFseeasvlellaeypnlvvlrT 207
                                               a++e++  + l +PnnPtG++l+ e+i+ +++ev da+V+vDeAY+eFs+e s+l l+ e pnl+vlrT
  lcl|NCBI__GCF_000020545.1:WP_012474521.1 158 AQEERAAFIVLSTPNNPTGKSLSIEDIRMIVHEV-DAIVLVDEAYVEFSREDSALCLIDEAPNLIVLRT 225
                                               *********************************9.9********************************* PP

                                 TIGR01141 208 lSKafgLAglRvGyaianaeiiealekvrapynvsslaleaavaalrdsdkiektveevkkererllee 276
                                               +SKa +LAg+R+G+a+ n+++  +++k + p+  s+la  +    l + + +e++v  + +erer++e+
  lcl|NCBI__GCF_000020545.1:WP_012474521.1 226 MSKALALAGMRIGFALTNPALLAEIAKPKIPFTSSRLAEITLQHVLANYHLVEESVSYILQERERIYEA 294
                                               ********************************************************************* PP

                                 TIGR01141 277 lkkleglevyeSkaNFvlikvkedaeelleallekgiivRdlksaeglleeclRitvGtreenerllea 345
                                               lk ++gl+v+eS+aNF++i+v+ +a+e++  l  +gi+vR+++ + +l+++clR  +G r+en+ lle 
  lcl|NCBI__GCF_000020545.1:WP_012474521.1 295 LKGISGLHVFESDANFIIIRVR-NAQEVFSFLAGEGILVRNVSGY-PLMQNCLRFNIGLRKENDLLLEK 361
                                               *********************9.**********************.588*******************9 PP

                                 TIGR01141 346 lk 347
                                               l+
  lcl|NCBI__GCF_000020545.1:WP_012474521.1 362 LR 363
                                               97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (349 nodes)
Target sequences:                          1  (365 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: 00:00:00.01
# Mc/sec: 9.54
//
[ok]

This GapMind analysis is from Apr 10 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