Alignments for a candidate for hisC in Pedobacter sp. GW460-11-11-14-LB5

GapMind for Amino acid biosynthesis

Alignments for a candidate for hisC in Pedobacter sp. GW460-11-11-14-LB5

Align histidinol-phosphate aminotransferase (EC 2.6.1.9) (characterized)
to candidate CA265_RS03630 CA265_RS03630 histidinol-phosphate transaminase

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



>FitnessBrowser__Pedo557:CA265_RS03630
          Length = 346

 Score =  387 bits (994), Expect = e-112
 Identities = 192/345 (55%), Positives = 250/345 (72%), Gaps = 5/345 (1%)

Query: 4   LQELTRPNIWKLKPYSSARDEYKGAVASVFLDANENPYNLP----HNRYPDPMQWELKTL 59
           + +L R NI  L+PYS+ARDE+KG  ASVFLDANEN Y  P    +NRYPDP+Q +LK  
Sbjct: 3   INDLVRENIKNLRPYSTARDEFKGQ-ASVFLDANENSYGSPLPANYNRYPDPLQLDLKDA 61

Query: 60  LSKIKKVSPQHIFLGNGSDEAIDLVFRAFCEPEKDNVVAIDPTYGMYQVCADVNNVEYRK 119
           +SKIK V  ++ FLGNGSDEAIDL+FRAFC P KDNV+ + PTYGMY+V A++N+VE RK
Sbjct: 62  ISKIKGVPIENTFLGNGSDEAIDLLFRAFCNPGKDNVIVLPPTYGMYEVSANINDVEIRK 121

Query: 120 VLLDENFQFSAEKLLAATDERTKLIFLCSPNNPTGNDLLRSEIEKILREFEGLVILDEAY 179
           V L  NFQ   EK+    D+ TKLIF+CSPNNPTGN + R +IE IL  F G+V++DEAY
Sbjct: 122 VSLLPNFQLDMEKIAETIDKNTKLIFICSPNNPTGNSINREDIETILANFNGIVVVDEAY 181

Query: 180 NDFSEAPSFLEELDKYPNLVVFQTFSKAWGCAAIRLGMAFASEAIIGILSKIKYPYNVNQ 239
            +++   +F++EL +Y NLVV QTFSKAWG AA+RLGMAF+S  +I +L+KIK PYN+NQ
Sbjct: 182 INYARQKTFIQELTEYGNLVVLQTFSKAWGLAALRLGMAFSSTKVIDVLNKIKPPYNINQ 241

Query: 240 LTQQQAIAMLHKYYEIERWIKTLKEERDYLEEEFAKLSCTVRMYPSDSNFFLAKVTDAVK 299
            TQ  A   L    ++  WIK    ERD L +    L+   ++YPSD+NF L +VTDA+K
Sbjct: 242 ATQDLAFEALKNIAQVNDWIKESVAERDRLSKALTALNIVKKVYPSDANFILTEVTDALK 301

Query: 300 IYNYLVGEGIIVRNRHSISLCCNCLRVTVGTRVENNTLLAALKKY 344
           IY+ LV +GIIVR+R  ++LC  CLR+TVGT+ EN+ LL  L+ +
Sbjct: 302 IYDTLVDQGIIVRDRSKVTLCEGCLRITVGTKEENDKLLTVLENF 346


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: 413
Number of extensions: 14
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: 346
Length of database: 346
Length adjustment: 29
Effective length of query: 317
Effective length of database: 317
Effective search space:   100489
Effective search space used:   100489
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 CA265_RS03630 CA265_RS03630 (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.32313.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                  -----------
   1.2e-117  378.7   0.2   1.3e-117  378.5   0.2    1.0  1  lcl|FitnessBrowser__Pedo557:CA265_RS03630  CA265_RS03630 histidinol-phospha


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Pedo557:CA265_RS03630  CA265_RS03630 histidinol-phosphate transaminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  378.5   0.2  1.3e-117  1.3e-117       1     348 [.       8     345 ..       8     346 .] 0.97

  Alignments for each domain:
  == domain 1  score: 378.5 bits;  conditional E-value: 1.3e-117
                                  TIGR01141   1 rekikklepYqpgarelgekevvkLnsnEnPfgpsekvkealkeelkklhrYpdpqalelkealakyl 68 
                                                re+ik+l pY+++ +e+ +++ v L++nEn +g +      l  +  + +rYpdp +l+lk a++k  
  lcl|FitnessBrowser__Pedo557:CA265_RS03630   8 RENIKNLRPYSTARDEFKGQASVFLDANENSYGSP------LP-A--NYNRYPDPLQLDLKDAISKIK 66 
                                                799*********76677777***************......33.3..69******************* PP

                                  TIGR01141  69 gveeenillgnGsdelielliraflepg.davlvleptysmYevsakiagaevkevplkedgqedlea 135
                                                gv  en +lgnGsde+i+ll+raf++pg d+v+vl+pty mYevsa+i+++e+++v+l  ++q d+e+
  lcl|FitnessBrowser__Pedo557:CA265_RS03630  67 GVPIENTFLGNGSDEAIDLLFRAFCNPGkDNVIVLPPTYGMYEVSANINDVEIRKVSLLPNFQLDMEK 134
                                                ******************************************************************** PP

                                  TIGR01141 136 vleaakekvklvflasPnnPtGnllkreeiekvleevedalVVvDeAYieFseeasvlellaeypnlv 203
                                                ++e++++++kl+f++sPnnPtGn+++re+ie++l++  +++VVvDeAYi++++++++++ l+ey nlv
  lcl|FitnessBrowser__Pedo557:CA265_RS03630 135 IAETIDKNTKLIFICSPNNPTGNSINREDIETILANF-NGIVVVDEAYINYARQKTFIQELTEYGNLV 201
                                                ************************************8.9***************************** PP

                                  TIGR01141 204 vlrTlSKafgLAglRvGyaianaeiiealekvrapynvsslaleaavaalrdsdkiektveevkkere 271
                                                vl+T+SKa gLA+lR+G+a+++ ++i++l+k+++pyn+++ ++++a +al++ +++++ ++e+ +er+
  lcl|FitnessBrowser__Pedo557:CA265_RS03630 202 VLQTFSKAWGLAALRLGMAFSSTKVIDVLNKIKPPYNINQATQDLAFEALKNIAQVNDWIKESVAERD 269
                                                ******************************************************************** PP

                                  TIGR01141 272 rlleelkklegle.vyeSkaNFvlikvkedaeelleallekgiivRdlksaeglleeclRitvGtree 338
                                                rl ++l++l+ ++ vy+S+aNF+l +v  da +++++l+++giivRd +++  l+e+clRitvGt+ee
  lcl|FitnessBrowser__Pedo557:CA265_RS03630 270 RLSKALTALNIVKkVYPSDANFILTEVT-DALKIYDTLVDQGIIVRDRSKV-TLCEGCLRITVGTKEE 335
                                                ************9**************9.********************99.589************* PP

                                  TIGR01141 339 nerllealke 348
                                                n++ll++l++
  lcl|FitnessBrowser__Pedo557:CA265_RS03630 336 NDKLLTVLEN 345
                                                *******986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (349 nodes)
Target sequences:                          1  (346 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: 9.68
//
[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