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.9447.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: 9.55
//
[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:

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:

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:

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:

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