Alignments for a candidate for hisC in Dechlorosoma suillum PS

GapMind for Amino acid biosynthesis

Alignments for a candidate for hisC in Dechlorosoma suillum PS

Align histidinol-phosphate aminotransferase (EC 2.6.1.9) (characterized)
to candidate Dsui_1414 Dsui_1414 histidinol-phosphate aminotransferase

Query= reanno::psRCH2:GFF3234
         (348 letters)



>FitnessBrowser__PS:Dsui_1414
          Length = 395

 Score =  490 bits (1262), Expect = e-143
 Identities = 253/353 (71%), Positives = 287/353 (81%), Gaps = 6/353 (1%)

Query: 1   MSKFWSPFVKDLVPYVPGEQPKLSKLVKLNTNENPYGPSPRAIAAMQAELND---SLRLY 57
           MSKFWSP V  L PYVPGEQPKL  LVKLNTNENPY PSP+ +AAMQAE+     SLRLY
Sbjct: 38  MSKFWSPLVNRLTPYVPGEQPKLPNLVKLNTNENPYPPSPKTVAAMQAEIGHDGASLRLY 97

Query: 58  PDPNGERLKQAVADYYG---VQPAQVFVGNGSDEVLAHAFHGLFQHAGPLLFPDISYSFY 114
           PDP+ +RLK+AVA +YG   +   QVFVGNGSDEVLAH F  L QH  PLL+PDISYSFY
Sbjct: 98  PDPSADRLKEAVAAFYGEFGIGARQVFVGNGSDEVLAHVFMALLQHDAPLLYPDISYSFY 157

Query: 115 PVYCGLYGIAYETVALDEQFQIDVADYNRPNGGIIFPNPNAPTGCLLALEAIERLLQANT 174
           PVY GLYGI+ ETVALD  + ID++ Y R NGGIIFPNPNAPTG LL L  IE LL ANT
Sbjct: 158 PVYAGLYGISAETVALDGDYGIDLSAYRRANGGIIFPNPNAPTGRLLPLGEIEALLTANT 217

Query: 175 ETVVLVDEAYVDFGGESAIALVDRYPNLLVTQTLSKSRSLAGLRVGLAVGHPDLIEALER 234
           E+VV+VDEAYVDFGG++AIALV+R+PNLLV  TLSKSRSLAGLRVG AVGHPDLIEALER
Sbjct: 218 ESVVVVDEAYVDFGGDTAIALVNRFPNLLVVHTLSKSRSLAGLRVGYAVGHPDLIEALER 277

Query: 235 IKNSFNSYPLDRIAIAGAAAAFEDRAYFQQTCQQVIDSREAVVAAMQGLGFEVLPSAANF 294
           +KNSFNSYPLDRIAIAGA AA EDRA+F +T   VI SRE +V+ +  LGF+VLPSAANF
Sbjct: 278 VKNSFNSYPLDRIAIAGAVAALEDRAWFDRTRNAVIASREQLVSDLTLLGFQVLPSAANF 337

Query: 295 IFARHPQRDAATIAASLREQGVIVRHFKQRRIEQFLRITIGTPEQNQALLEAL 347
           +FARHP RD A +A +LR++ +IVRHFK  RI+QFLRITIGT EQ  AL+ AL
Sbjct: 338 VFARHPGRDGAELAQALRQRSIIVRHFKAPRIDQFLRITIGTDEQCGALVAAL 390


Lambda     K      H
   0.320    0.137    0.401 

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: 544
Number of extensions: 22
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: 348
Length of database: 395
Length adjustment: 30
Effective length of query: 318
Effective length of database: 365
Effective search space:   116070
Effective search space used:   116070
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 Dsui_1414 Dsui_1414 (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.31535.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
    6.8e-92  294.0   0.0    7.7e-92  293.8   0.0    1.0  1  lcl|FitnessBrowser__PS:Dsui_1414  Dsui_1414 histidinol-phosphate a


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__PS:Dsui_1414  Dsui_1414 histidinol-phosphate aminotransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  293.8   0.0   7.7e-92   7.7e-92       4     349 .]      46     393 ..      43     393 .. 0.93

  Alignments for each domain:
  == domain 1  score: 293.8 bits;  conditional E-value: 7.7e-92
                         TIGR01141   4 ikklepYqpgarelgekevvkLnsnEnPfgpsekvkealkeelk....klhrYpdpqalelkealakylg...veee 73 
                                       ++ l+pY+pg++ +   + vkLn+nEnP++ps+k ++a+++e+     +l++Ypdp+a +lkea+a+++g   +++ 
  lcl|FitnessBrowser__PS:Dsui_1414  46 VNRLTPYVPGEQPKLP-NLVKLNTNENPYPPSPKTVAAMQAEIGhdgaSLRLYPDPSADRLKEAVAAFYGefgIGAR 121
                                       789******9666555.6*************************888999*******************99999**** PP

                         TIGR01141  74 nillgnGsdelielliraflepgdavlvleptysmYevsakiagaevkevplkedgqedleavleaakekvklvfla 150
                                       ++++gnGsde++  +++a+l+  +  l+++ +ys Y+v+a ++g++  +v+l+ d   dl a       +   + + 
  lcl|FitnessBrowser__PS:Dsui_1414 122 QVFVGNGSDEVLAHVFMALLQHDAPLLYPDISYSFYPVYAGLYGISAETVALDGDYGIDLSAYR---RANGG-IIFP 194
                                       *******************************************************656666665...33334.5569 PP

                         TIGR01141 151 sPnnPtGnllkreeiekvleevedalVVvDeAYieFseeasvlellaeypnlvvlrTlSKafgLAglRvGyaianae 227
                                       +Pn+PtG ll   eie++l + ++ +VVvDeAY++F ++ +++ l++++pnl+v+ TlSK+ +LAglRvGya+++++
  lcl|FitnessBrowser__PS:Dsui_1414 195 NPNAPTGRLLPLGEIEALLTANTESVVVVDEAYVDFGGD-TAIALVNRFPNLLVVHTLSKSRSLAGLRVGYAVGHPD 270
                                       *******************99889**************8.************************************* PP

                         TIGR01141 228 iiealekvrapyn...vsslaleaavaalrdsdkiektveevkkererlleelkkleglevyeSkaNFvlikvke.d 300
                                       +ieale+v++++n   ++++a + avaal+d++ + +t ++v+++re+l + l+ l g++v +S aNFv+++ +  d
  lcl|FitnessBrowser__PS:Dsui_1414 271 LIEALERVKNSFNsypLDRIAIAGAVAALEDRAWFDRTRNAVIASREQLVSDLTLL-GFQVLPSAANFVFARHPGrD 346
                                       *********87543339*************************************99.8***************999* PP

                         TIGR01141 301 aeelleallekgiivRdlksaeglleeclRitvGtreenerllealkei 349
                                        +el++al ++ iivR++k+  + ++++lRit+Gt+e++ +l++alkei
  lcl|FitnessBrowser__PS:Dsui_1414 347 GAELAQALRQRSIIVRHFKA--PRIDQFLRITIGTDEQCGALVAALKEI 393
                                       ******************94..468*********************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (349 nodes)
Target sequences:                          1  (395 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: 8.30
//
[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