GapMind for catabolism of small carbon sources

 

Alignments for a candidate for garR in Desulfovibrio vulgaris Miyazaki F

Align 2-hydroxy-3-oxopropionate reductase; Tartronate semialdehyde reductase; TSAR; EC 1.1.1.60 (characterized)
to candidate 8502217 DvMF_2927 tartronate semialdehyde reductase (RefSeq)

Query= SwissProt::P0ABQ2
         (294 letters)



>FitnessBrowser__Miya:8502217
          Length = 299

 Score =  365 bits (936), Expect = e-106
 Identities = 192/293 (65%), Positives = 222/293 (75%)

Query: 2   KVGFIGLGIMGKPMSKNLLKAGYSLVVADRNPEAIADVIAAGAETASTAKAIAEQCDVII 61
           ++GFIGLGIMG PM +NLLKAG+ +    RN + +  + A GA  A +  A+A   DV+I
Sbjct: 3   RIGFIGLGIMGAPMCRNLLKAGFPVTAYTRNGDKLRAMAAEGAAAAESPAAVAAASDVVI 62

Query: 62  TMLPNSPHVKEVALGENGIIEGAKPGTVLIDMSSIAPLASREISEALKAKGIDMLDAPVS 121
           TMLPNSP V+ VALG  GI EGA PG ++ DMSSIAPLASREI+  L  K I MLDAPVS
Sbjct: 63  TMLPNSPEVRAVALGPGGIAEGAAPGCIVADMSSIAPLASREIAAELAKKSIRMLDAPVS 122

Query: 122 GGEPKAIDGTLSVMVGGDKAIFDKYYDLMKAMAGSVVHTGEIGAGNVTKLANQVIVALNI 181
           GGEPKAIDGTLSVMVGG +  FD    + KAMA SVV  GE+GAGNVTKLANQ++VA NI
Sbjct: 123 GGEPKAIDGTLSVMVGGAQEDFDACLPVFKAMAASVVRVGEVGAGNVTKLANQIVVAGNI 182

Query: 182 AAMSEALTLATKAGVNPDLVYQAIRGGLAGSTVLDAKAPMVMDRNFKPGFRIDLHIKDLA 241
           AAMSEAL LAT+AG +PDLVYQAIRGGLAGSTVLDAKAP+VMD  F PGFRI LH KD+ 
Sbjct: 183 AAMSEALVLATRAGADPDLVYQAIRGGLAGSTVLDAKAPLVMDGRFTPGFRIRLHAKDMG 242

Query: 242 NALDTSHGVGAQLPLTAAVMEMMQALRADGLGTADHSALACYYEKLAKVEVTR 294
           N L+TS  +   LPL A +ME+MQ L ADGLG ADH AL  ++EKLA VEV R
Sbjct: 243 NVLETSRELHVPLPLAAQLMEVMQGLMADGLGDADHGALIRHWEKLAGVEVRR 295


Lambda     K      H
   0.316    0.133    0.366 

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: 329
Number of extensions: 5
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: 294
Length of database: 299
Length adjustment: 26
Effective length of query: 268
Effective length of database: 273
Effective search space:    73164
Effective search space used:    73164
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 48 (23.1 bits)

Align candidate 8502217 DvMF_2927 (tartronate semialdehyde reductase (RefSeq))
to HMM TIGR01505 (2-hydroxy-3-oxopropionate reductase (EC 1.1.1.60))

# 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/TIGR01505.hmm
# target sequence database:        /tmp/gapView.14384.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01505  [M=291]
Accession:   TIGR01505
Description: tartro_sem_red: 2-hydroxy-3-oxopropionate reductase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   3.4e-122  393.2   9.1   3.8e-122  393.0   9.1    1.0  1  lcl|FitnessBrowser__Miya:8502217  DvMF_2927 tartronate semialdehyd


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Miya:8502217  DvMF_2927 tartronate semialdehyde reductase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  393.0   9.1  3.8e-122  3.8e-122       1     291 []       3     293 ..       3     293 .. 0.99

  Alignments for each domain:
  == domain 1  score: 393.0 bits;  conditional E-value: 3.8e-122
                         TIGR01505   1 kvgfiGlGimGkPmsknllkaGyqlvvatleqealdellaaGaesaetakevvedadvivtmvPdsPqveevalGen 77 
                                       ++gfiGlGimG Pm++nllkaG+ +++ t++ ++l  ++a Ga +ae+ ++v+ ++dv++tm+P+sP+v++valG+ 
  lcl|FitnessBrowser__Miya:8502217   3 RIGFIGLGIMGAPMCRNLLKAGFPVTAYTRNGDKLRAMAAEGAAAAESPAAVAAASDVVITMLPNSPEVRAVALGPG 79 
                                       58*************************************************************************** PP

                         TIGR01505  78 GileaakkGkvlvdmssiaPleskelakavkekGidvldaPvsGGeagaiegtlsimvGGdkavfdkvkpllealgk 154
                                       Gi e+a +G ++ dmssiaPl+s+e+a ++ +k i++ldaPvsGGe++ai+gtls+mvGG + +fd   p+++a++ 
  lcl|FitnessBrowser__Miya:8502217  80 GIAEGAAPGCIVADMSSIAPLASREIAAELAKKSIRMLDAPVSGGEPKAIDGTLSVMVGGAQEDFDACLPVFKAMAA 156
                                       ***************************************************************************** PP

                         TIGR01505 155 sivlvGenGaGqtvkvanqvivalnieavsealvlaekaGvdpkavlqalrGGlagstvleakkerlldrdfkPGfr 231
                                       s+v vGe GaG+++k+anq++va ni+a+sealvla++aG+dp++v+qa+rGGlagstvl+ak++ ++d  f PGfr
  lcl|FitnessBrowser__Miya:8502217 157 SVVRVGEVGAGNVTKLANQIVVAGNIAAMSEALVLATRAGADPDLVYQAIRGGLAGSTVLDAKAPLVMDGRFTPGFR 233
                                       ***************************************************************************** PP

                         TIGR01505 232 idlhqkdlalaldaakavgaalPvtavvaellaalradGdgtldhsalvraleklakdkv 291
                                       i lh kd++++l++++++ + lP++a  +e+++ l adG g++dh al+r  ekla+++v
  lcl|FitnessBrowser__Miya:8502217 234 IRLHAKDMGNVLETSRELHVPLPLAAQLMEVMQGLMADGLGDADHGALIRHWEKLAGVEV 293
                                       ********************************************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (291 nodes)
Target sequences:                          1  (299 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 0.00s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 11.25
//
[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:

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