Alignments for a candidate for deoA in Shewanella amazonensis SB2B

GapMind for catabolism of small carbon sources

Alignments for a candidate for deoA in Shewanella amazonensis SB2B

Align thymidine phosphorylase (EC 2.4.2.4) (characterized)
to candidate 6936792 Sama_0974 thymidine phosphorylase (RefSeq)

Query= BRENDA::Q7CP66
         (440 letters)



>FitnessBrowser__SB2B:6936792
          Length = 443

 Score =  601 bits (1549), Expect = e-176
 Identities = 295/438 (67%), Positives = 358/438 (81%)

Query: 1   MFLAQEIIRKKRDGHALSDEEIRFFINGIRDNTISEGQIAALAMTIFFHDMTMPERVSLT 60
           MFLAQEIIRKKR+  ALS EEI+FF+ GI DN++SEGQIAAL M ++F+DMTM ER++LT
Sbjct: 1   MFLAQEIIRKKRNAEALSKEEIQFFVKGITDNSVSEGQIAALGMAVYFNDMTMDERIALT 60

Query: 61  MAMRDSGTVLDWKSLNLNGPIVDKHSTGGVGDVTSLMLGPMVAACGGYVPMISGRGLGHT 120
            AMRDSGTVL+W SL LNGP++DKHSTGGVGDV SLMLGPM AACGGYVPMISGRGLGHT
Sbjct: 61  TAMRDSGTVLNWDSLGLNGPVIDKHSTGGVGDVISLMLGPMAAACGGYVPMISGRGLGHT 120

Query: 121 GGTLDKLEAIPGFDIFPDDNRFREIIQDVGVAIIGQTSSLAPADKRFYATRDITATVDSI 180
           GGTLDK +AIPG+   P    FR+++++ GVAIIGQT  L PADKRFY+ RD TATV+SI
Sbjct: 121 GGTLDKFDAIPGYQTEPSSELFRKVVKEAGVAIIGQTGDLVPADKRFYSIRDNTATVESI 180

Query: 181 PLITGSILAKKLAEGLDALVMDVKVGSGAFMPTYELSEALAEAIVGVANGAGVRTTALLT 240
            LIT SIL+KKLA GLDAL MDVKVGSGAFMPTYE S  LA +I  VANGAG +TTALLT
Sbjct: 181 SLITASILSKKLAAGLDALAMDVKVGSGAFMPTYEASLELARSITAVANGAGTKTTALLT 240

Query: 241 DMNQVLASSAGNAVEVREAVQFLTGEYRNPRLFDVTMALCVEMLISGQLAKDDAEARAKL 300
           DMNQVLAS AGNA+EV+EAV FLTG+YRNPRL++VTM LC EML+ G LA +DA+AR KL
Sbjct: 241 DMNQVLASCAGNALEVKEAVDFLTGKYRNPRLYEVTMGLCAEMLVLGGLAANDADARTKL 300

Query: 301 QAVLDNGKAAEVFGRMVAAQKGPSDFVENYDKYLPTAMLSKAVYADTEGFISAMDTRALG 360
             VLDNG+AAE+FG+MV+   GP+DFVE+YDKYLP A + + VYA+ +GF  +M TR LG
Sbjct: 301 NTVLDNGRAAEIFGKMVSGLGGPADFVESYDKYLPKASIIRPVYAERDGFAYSMVTRELG 360

Query: 361 MAVVSMGGGRRQASDTIDYSVGFTDMARLGDSIDGQRPLAVIHAKDEASWQEAAKAVKAA 420
           +AVV++GGGRR+  D +DYSVG +++  LG  I+   PLAVIHA+ EA+++EAA+AV+ A
Sbjct: 361 LAVVTLGGGRRKPGDALDYSVGLSNVCALGQPINKDTPLAVIHAQSEAAFEEAARAVRGA 420

Query: 421 IILDDKAPASTPSVYRRI 438
           I + DK P  TP +Y+ +
Sbjct: 421 ITVSDKQPEKTPEIYQYV 438


Lambda     K      H
   0.319    0.134    0.377 

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: 609
Number of extensions: 14
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: 440
Length of database: 443
Length adjustment: 32
Effective length of query: 408
Effective length of database: 411
Effective search space:   167688
Effective search space used:   167688
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 (21.7 bits)
S2: 51 (24.3 bits)

Align candidate 6936792 Sama_0974 (thymidine phosphorylase (RefSeq))
to HMM TIGR02643 (deoA: thymidine phosphorylase (EC 2.4.2.4))

# 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.carbon/TIGR02643.hmm
# target sequence database:        /tmp/gapView.8375.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR02643  [M=437]
Accession:   TIGR02643
Description: T_phosphoryl: thymidine phosphorylase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   5.9e-224  729.7   3.6   6.8e-224  729.5   3.6    1.0  1  lcl|FitnessBrowser__SB2B:6936792  Sama_0974 thymidine phosphorylas


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__SB2B:6936792  Sama_0974 thymidine phosphorylase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  729.5   3.6  6.8e-224  6.8e-224       1     436 [.       2     437 ..       2     438 .. 1.00

  Alignments for each domain:
  == domain 1  score: 729.5 bits;  conditional E-value: 6.8e-224
                         TIGR02643   1 llpqeiirkkrdglslsdeeiaafvegvtddsvsegqiaalamavyfngleldekvaltlamrdsGdvldwkdldln 77 
                                       +l+qeiirkkr++++ls+eei+ fv+g+td+svsegqiaal mavyfn++++de++alt amrdsG+vl+w +l ln
  lcl|FitnessBrowser__SB2B:6936792   2 FLAQEIIRKKRNAEALSKEEIQFFVKGITDNSVSEGQIAALGMAVYFNDMTMDERIALTTAMRDSGTVLNWDSLGLN 78 
                                       79*************************************************************************** PP

                         TIGR02643  78 gPvvdkhstGGvGdvvslmlaPivaacGgyvPmisGrGlGhtGGtldkleaiPGydvaPdeelfrkvvkdvGvaiiG 154
                                       gPv+dkhstGGvGdv+slml+P+ aacGgyvPmisGrGlGhtGGtldk++aiPGy++ P++elfrkvvk++GvaiiG
  lcl|FitnessBrowser__SB2B:6936792  79 GPVIDKHSTGGVGDVISLMLGPMAAACGGYVPMISGRGLGHTGGTLDKFDAIPGYQTEPSSELFRKVVKEAGVAIIG 155
                                       ***************************************************************************** PP

                         TIGR02643 155 qtadlaPadkrlyairdvtatvesiplitasilskklaaGldalvldvkvGnGafmesleeseelarslvevangaG 231
                                       qt+dl Padkr+y+ird tatvesi+litasilskklaaGldal++dvkvG+Gafm+++e s elars+  vangaG
  lcl|FitnessBrowser__SB2B:6936792 156 QTGDLVPADKRFYSIRDNTATVESISLITASILSKKLAAGLDALAMDVKVGSGAFMPTYEASLELARSITAVANGAG 232
                                       ***************************************************************************** PP

                         TIGR02643 232 vrttalitdmnqalasaaGnavevreavdfltGekrdkrleevtlalaaellvsgklaadeaeaeakleavlesGra 308
                                        +ttal+tdmnq+las+aGna+ev+eavdfltG++r++rl evt+ l+ae+lv g+laa++a+a++kl++vl++Gra
  lcl|FitnessBrowser__SB2B:6936792 233 TKTTALLTDMNQVLASCAGNALEVKEAVDFLTGKYRNPRLYEVTMGLCAEMLVLGGLAANDADARTKLNTVLDNGRA 309
                                       ***************************************************************************** PP

                         TIGR02643 309 aerfarmvaalgGPadfvekpekylakaaiakavkaaregylseidtrelGlavvalGGGrrkaddkldlsvGltdl 385
                                       ae+f++mv+ lgGPadfve ++kyl+ka+i+++v+a+r+g+  ++ trelGlavv+lGGGrrk+ d ld+svGl+++
  lcl|FitnessBrowser__SB2B:6936792 310 AEIFGKMVSGLGGPADFVESYDKYLPKASIIRPVYAERDGFAYSMVTRELGLAVVTLGGGRRKPGDALDYSVGLSNV 386
                                       ***************************************************************************** PP

                         TIGR02643 386 lelGekvekeeplavvhaadeedaeeaakavkkalkiadeaPeeakvvler 436
                                         lG+ ++k++plav+ha++e+ +eeaa+av+ a++++d++Pe+++ +++ 
  lcl|FitnessBrowser__SB2B:6936792 387 CALGQPINKDTPLAVIHAQSEAAFEEAARAVRGAITVSDKQPEKTPEIYQY 437
                                       ***********************************************9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (437 nodes)
Target sequences:                          1  (443 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: 00:00:00.02
# Mc/sec: 7.97
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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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, or view the source code.

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 catabolism of small carbon sources