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

GapMind for catabolism of small carbon sources

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

Align Ribose import ATP-binding protein RbsA 2, component of D-ribose porter (Nanavati et al., 2006). Induced by ribose (characterized)
to candidate 3607108 Dshi_0530 ABC transporter related (RefSeq)

Query= TCDB::Q9X051
         (523 letters)



>FitnessBrowser__Dino:3607108
          Length = 498

 Score =  344 bits (882), Expect = 5e-99
 Identities = 192/493 (38%), Positives = 298/493 (60%), Gaps = 10/493 (2%)

Query: 13  LEARNITKTFPGVIAVNNVTLQIYKGEVCALVGENGAGKSTLMKILAGVYPDYEGQIFLE 72
           ++ R ITK + GV A+++V   +  GE   L GENG+GKSTL+KI++GV P   G + + 
Sbjct: 10  IDLRAITKRYAGVTALDSVDFTVQPGEAVCLAGENGSGKSTLIKIISGVEPATAGTVQIA 69

Query: 73  GKEVRFRNPREAQENGIALIPQELDLVPNLSSAENIFLSREPVNEFGVIEYQKMFEQASK 132
           G+E    NPR +   G+ +I Q+  L PNLS AENI  + +      + +++ + + A  
Sbjct: 70  GQEHVTLNPRISAAAGVMVIFQDFSLFPNLSVAENIAFTTQLSTRQRLFKFRAVRDIARA 129

Query: 133 LFSKLGVNIDPKTKVEDLSTSQQQMVAIAKALSLDAKIIIMDEPTSAIGKRETEQLFNII 192
              ++GV ID   +VE L  +Q+Q+VAI +AL+  A++IIMDEPT+A+ ++E  +L  II
Sbjct: 130 ALDRIGVQIDLDARVETLPVAQKQLVAICRALASKAQLIIMDEPTTALTEKEVRRLQGII 189

Query: 193 RSLKNEGKSVIYISHRLEEIFEIADRVVVMRDGRKVGEGPIEEFDHDKLVRLMVGRSIDQ 252
           R LK EG +VI++SH+L E+ E++++VVV+R+G+KV EGP  EFD   L   M GR + +
Sbjct: 190 RMLKEEGVAVIFVSHKLAEVLEVSEKVVVLRNGKKVAEGPASEFDTQSLTYHMTGRDVPE 249

Query: 253 FFIKERATITDEIFRVEGIKLWSLDRKKLLVDDVSFYVRKGEVLGIYGLVGAGRTELLEA 312
               + A     + +V+G+       K     D+SF +R GEVLGI GL+G GRT + +A
Sbjct: 250 VPPSDVAAGAQTLMQVQGL------GKAGSFSDISFDLRTGEVLGITGLLGCGRTSVAKA 303

Query: 313 IFGAHPGRTEGKVFIGGKEIKIHSPRDAVKNGIGLVPEDRKTAGLILQMSVLHNITLPSV 372
           +FG       G + + G  + +  P+ A    IG VPEDR T GL L  S+L N+ +  +
Sbjct: 304 LFGL-VTPDAGSILVDGSPVPLGDPQAASLARIGYVPEDRLTEGLFLSQSILRNVAVGRL 362

Query: 373 VMKLIVRKFGLIDSQLEKEIVRSFIEKLNIKTPSPYQIVENLSGGNQQKVVLAKWLAIKP 432
                    G +D     +    ++ +L +K P     V++LSGGNQQ+V LA+WL+  P
Sbjct: 363 DAH---TSGGFLDMTGLAKEASDWLRRLKVKAPDVEAPVQSLSGGNQQRVALARWLSRAP 419

Query: 433 KVLLLDEPTRGIDVNAKSEIYKLISEMAVSGMGVVMVSSELPEILAMSDRILVMSEGRKT 492
           +VL+L+ P+ G+DV +K++I+ +I E+A  G+GV+++S +LPE+LA   R+LVM EGR  
Sbjct: 420 RVLILNGPSVGVDVGSKADIHDIIRELAREGIGVIVISDDLPELLATCHRVLVMREGRII 479

Query: 493 AEFLREEVTEEDL 505
                  +TE+DL
Sbjct: 480 DALEGTALTEDDL 492


Lambda     K      H
   0.317    0.137    0.372 

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: 534
Number of extensions: 30
Number of successful extensions: 8
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: 523
Length of database: 498
Length adjustment: 34
Effective length of query: 489
Effective length of database: 464
Effective search space:   226896
Effective search space used:   226896
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: 52 (24.6 bits)

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

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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