Alignments for a candidate for rhaA in Dinoroseobacter shibae DFL-12

GapMind for catabolism of small carbon sources

Alignments for a candidate for rhaA in Dinoroseobacter shibae DFL-12

Align L-rhamnose isomerase (EC 5.3.1.14) (characterized)
to candidate 3609048 Dshi_2437 L-rhamnose isomerase (RefSeq)

Query= reanno::Dino:3609048
         (412 letters)



>FitnessBrowser__Dino:3609048
          Length = 412

 Score =  836 bits (2160), Expect = 0.0
 Identities = 412/412 (100%), Positives = 412/412 (100%)

Query: 1   MGYENAKAAFAEWGVDTEAALARLKTIPISMHCWQGDDVVGFEQKTGSSGGGIQATGNHP 60
           MGYENAKAAFAEWGVDTEAALARLKTIPISMHCWQGDDVVGFEQKTGSSGGGIQATGNHP
Sbjct: 1   MGYENAKAAFAEWGVDTEAALARLKTIPISMHCWQGDDVVGFEQKTGSSGGGIQATGNHP 60

Query: 61  GRARTPDELRADLEFAYAMIPGRHRLNLHAMYLDTEATPDRDEIEIAHFAPWVDWARAQG 120
           GRARTPDELRADLEFAYAMIPGRHRLNLHAMYLDTEATPDRDEIEIAHFAPWVDWARAQG
Sbjct: 61  GRARTPDELRADLEFAYAMIPGRHRLNLHAMYLDTEATPDRDEIEIAHFAPWVDWARAQG 120

Query: 121 IGLDFNPTFFAHAKADDNLTLSHPDPGIRDFWIEHGKRSREIAAGMGAALGSACVNNIWV 180
           IGLDFNPTFFAHAKADDNLTLSHPDPGIRDFWIEHGKRSREIAAGMGAALGSACVNNIWV
Sbjct: 121 IGLDFNPTFFAHAKADDNLTLSHPDPGIRDFWIEHGKRSREIAAGMGAALGSACVNNIWV 180

Query: 181 PDGYKDTPVDRMAARARLEASLDAMLAPPQDRARMLDAVESKLFGIGVEACTVGSHEFYM 240
           PDGYKDTPVDRMAARARLEASLDAMLAPPQDRARMLDAVESKLFGIGVEACTVGSHEFYM
Sbjct: 181 PDGYKDTPVDRMAARARLEASLDAMLAPPQDRARMLDAVESKLFGIGVEACTVGSHEFYM 240

Query: 241 GYAIRKGTLLCLDMGHFHPTENIADKLSAVALSLDEILLHVSRPMRWDSDHVILLDDDIL 300
           GYAIRKGTLLCLDMGHFHPTENIADKLSAVALSLDEILLHVSRPMRWDSDHVILLDDDIL
Sbjct: 241 GYAIRKGTLLCLDMGHFHPTENIADKLSAVALSLDEILLHVSRPMRWDSDHVILLDDDIL 300

Query: 301 QMAQELVSADLLGRTRIGLDFFDATISRTAAWVIGTRNMQKALLRALLMPLDRLRAAEDA 360
           QMAQELVSADLLGRTRIGLDFFDATISRTAAWVIGTRNMQKALLRALLMPLDRLRAAEDA
Sbjct: 301 QMAQELVSADLLGRTRIGLDFFDATISRTAAWVIGTRNMQKALLRALLMPLDRLRAAEDA 360

Query: 361 LDFTTRLVVTEEVKDLPFGAVWAEFAAREDVPNGQKLIRELDRYQAQVSGRG 412
           LDFTTRLVVTEEVKDLPFGAVWAEFAAREDVPNGQKLIRELDRYQAQVSGRG
Sbjct: 361 LDFTTRLVVTEEVKDLPFGAVWAEFAAREDVPNGQKLIRELDRYQAQVSGRG 412


Lambda     K      H
   0.321    0.137    0.420 

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: 787
Number of extensions: 19
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: 412
Length of database: 412
Length adjustment: 31
Effective length of query: 381
Effective length of database: 381
Effective search space:   145161
Effective search space used:   145161
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 (21.9 bits)
S2: 50 (23.9 bits)

Align candidate 3609048 Dshi_2437 (L-rhamnose isomerase (RefSeq))
to HMM TIGR01748 (rhaA: L-rhamnose isomerase (EC 5.3.1.14))

# 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/TIGR01748.hmm
# target sequence database:        /tmp/gapView.31716.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01748  [M=414]
Accession:   TIGR01748
Description: rhaA: L-rhamnose isomerase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
     3e-187  608.8   0.0   3.6e-187  608.5   0.0    1.0  1  lcl|FitnessBrowser__Dino:3609048  Dshi_2437 L-rhamnose isomerase (


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Dino:3609048  Dshi_2437 L-rhamnose isomerase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  608.5   0.0  3.6e-187  3.6e-187       5     410 ..       3     408 ..       1     411 [. 0.99

  Alignments for each domain:
  == domain 1  score: 608.5 bits;  conditional E-value: 3.6e-187
                         TIGR01748   5 yevakqryeavgidveealrqledvkislhcwqgddvegfenpegeltggiqatgnypgkartaeelrrdlekalsl 81 
                                       ye ak +++++g+d+e al +l+ ++is+hcwqgddv gfe++ g+  ggiqatgn+pg+art++elr+dle a+++
  lcl|FitnessBrowser__Dino:3609048   3 YENAKAAFAEWGVDTEAALARLKTIPISMHCWQGDDVVGFEQKTGSSGGGIQATGNHPGRARTPDELRADLEFAYAM 79 
                                       99*************************************************************************** PP

                         TIGR01748  82 ipgkkrlnlhaiyvetdekverdeikpkhfknwvewakeqglgldfnptlfshelaadgltlshadkeirefwiehc 158
                                       ipg++rlnlha+y++t+ + +rdei+  hf +wv+wa++qg+gldfnpt+f+h +a d+ltlsh+d+ ir+fwieh+
  lcl|FitnessBrowser__Dino:3609048  80 IPGRHRLNLHAMYLDTEATPDRDEIEIAHFAPWVDWARAQGIGLDFNPTFFAHAKADDNLTLSHPDPGIRDFWIEHG 156
                                       ***************************************************************************** PP

                         TIGR01748 159 kasrriseyfgkelgtpsvtniwipdglkdipvdrltprkrllealdevlsekldekytldavesklfglgaesytv 235
                                       k+sr i++ +g  lg+++v+niw+pdg+kd pvdr++ r rl ++ld +l+   d +  ldavesklfg+g e+ tv
  lcl|FitnessBrowser__Dino:3609048 157 KRSREIAAGMGAALGSACVNNIWVPDGYKDTPVDRMAARARLEASLDAMLAPPQDRARMLDAVESKLFGIGVEACTV 233
                                       ***************************************************************************** PP

                         TIGR01748 236 gshefylgyaltrdklllldaghfhptevisnkisslllyskklllhvsrpvrwdsdhvvvlddelreiaseivrnd 312
                                       gshefy+gya+ + +ll+ld ghfhpte i++k+s+++l  +++llhvsrp+rwdsdhv++ldd++ ++a+e+v  d
  lcl|FitnessBrowser__Dino:3609048 234 GSHEFYMGYAIRKGTLLCLDMGHFHPTENIADKLSAVALSLDEILLHVSRPMRWDSDHVILLDDDILQMAQELVSAD 310
                                       ***************************************************************************** PP

                         TIGR01748 313 llekvaigldffdasinriaawvigtrnmkkallkalleptadlkkleeegdyterlalleelkslpfgavwesyce 389
                                       ll++++igldffda+i r aawvigtrnm+kall+all p   l+  e + d+t+rl ++ee+k+lpfgavw  +  
  lcl|FitnessBrowser__Dino:3609048 311 LLGRTRIGLDFFDATISRTAAWVIGTRNMQKALLRALLMPLDRLRAAEDALDFTTRLVVTEEVKDLPFGAVWAEFAA 387
                                       ***************************************************************************** PP

                         TIGR01748 390 rkgvpvgeewlkevkayekev 410
                                       r++vp g++ ++e+  y+ +v
  lcl|FitnessBrowser__Dino:3609048 388 REDVPNGQKLIRELDRYQAQV 408
                                       *****************9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (414 nodes)
Target sequences:                          1  (412 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.02
# Mc/sec: 8.22
//
[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
the source code
instructions for running GapMind on your computer

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