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 ABC-type sugar transport system, ATPase component protein (characterized, see rationale)
to candidate 3607097 Dshi_0519 ABC transporter related (RefSeq)

Query= uniprot:D8IUD1
         (522 letters)



>FitnessBrowser__Dino:3607097
          Length = 498

 Score =  285 bits (730), Expect = 2e-81
 Identities = 187/473 (39%), Positives = 260/473 (54%), Gaps = 10/473 (2%)

Query: 16  LSGIGKRYAAP-VLDGIDLDLRPGQVLALTGENGAGKSTLSKIICGLVDASAGGMMLDGQ 74
           ++G+ K +    VL GIDL L PG V  L G NGAGKSTL K+ICG   A  G M L   
Sbjct: 1   MNGLQKSFGKNNVLRGIDLTLDPGSVTVLMGANGAGKSTLVKVICGQHRADGGTMRLATN 60

Query: 75  PYAPASRTQAEGLGIRMVMQELN--LIPTLSIAENLFLEKLPRR-FGWIDRKKLAEAARA 131
            + P     A   G+  V Q ++  +IP L +A NL L++L     G   R++      A
Sbjct: 61  AFDPEDAADAIRQGVVTVHQSIDDGVIPDLDVANNLMLDRLAEHSHGLFVRERHLRTEAA 120

Query: 132 QMEVVGLGELDPWTPVGDLGLGHQQMVEIARNLIGSCRCLILDEPTAMLTNREVELLFSR 191
           ++      E++    V DL +  +QM+ IAR +  + + LILDEPT+ L+  E + LF  
Sbjct: 121 KVAAAMGIEVNLRARVSDLSVADRQMIAIARAMARAPKVLILDEPTSSLSATEADRLFEL 180

Query: 192 IERLRAEGVAIIYISHRLEELKRIADRIVVLRDGKLVCNDDIGRYSTEQLVQLMAGELTK 251
           I+RLRA+GVAI+YISHR+ +++RIADRIVV+RDG +    +      E  V  M G    
Sbjct: 181 IDRLRAQGVAILYISHRMSDIRRIADRIVVMRDGMISGVFETEPLDLEAAVTAMLGH-RM 239

Query: 252 VDLDAEHRRIGAPVLRIRGLGRAPVVHPASLALHAGEVLGIAGLIGSGRTELLRLIFGAD 311
            ++DAE R+   PVL I+ L       P +L  H GEV+ + GL+GSG++ L  ++FG  
Sbjct: 240 TEVDAEVRQGTHPVLEIKNLQLFEGASPITLTAHDGEVVALVGLLGSGKSRLAEILFGIA 299

Query: 312 RAEQGEIFI-GDSQEPARIRSPKDAVKAGIAMVTEDRKGQGLLLPQAISVNTSLANLGSV 370
           R  +G I I G    P   RS KDA+  G+ M  +DR    ++    I+ N +L  L  +
Sbjct: 300 RPIRGSIRIKGKDYSP---RSVKDAIAQGVFMSPKDRGTNAVIPAFDIADNMTLPFLQGM 356

Query: 371 SRGGMLDHAAESSVAQDYVKKLRIRSGSVAQAAGELSGGNQQKVVIARWLYRDCPIMLFD 430
           S G  L    +   AQ  V +L I   SV    G LSGGNQQKV+IARWL     ++L D
Sbjct: 357 SVGSFLKSRQQRGTAQGMVDRLGIVCQSVRDGIGTLSGGNQQKVMIARWLLEPAQVLLLD 416

Query: 431 EPTRGIDIGAKSDIYRLFAELAAQGKGLLVVSSDLRELMQICDRIAVMSAGRI 483
           EP +G+DIGA+ DI         QG+  LV  +++ E ++I DRI VMS G I
Sbjct: 417 EPFQGVDIGARRDIGH-HIRATTQGRATLVFLAEIDEALEIADRIVVMSEGAI 468



 Score = 77.0 bits (188), Expect = 1e-18
 Identities = 66/260 (25%), Positives = 114/260 (43%), Gaps = 22/260 (8%)

Query: 269 RGLGRAPVVHPASLALHAGEVLGIAGLIGSGRTELLRLIFGADRAEQGEIFIGDSQ-EPA 327
           +  G+  V+    L L  G V  + G  G+G++ L+++I G  RA+ G + +  +  +P 
Sbjct: 6   KSFGKNNVLRGIDLTLDPGSVTVLMGANGAGKSTLVKVICGQHRADGGTMRLATNAFDP- 64

Query: 328 RIRSPKDAVKAGIAMVTEDRKGQGLLLPQAISVNTSLANLGSVSRG------GMLDHAAE 381
                 DA++ G+  V +     G++    ++ N  L  L   S G       +   AA+
Sbjct: 65  --EDAADAIRQGVVTVHQSID-DGVIPDLDVANNLMLDRLAEHSHGLFVRERHLRTEAAK 121

Query: 382 SSVAQDYVKKLRIRSGSVAQAAGELSGGNQQKVVIARWLYRDCPIMLFDEPTRGIDIGAK 441
            + A      LR R         +LS  ++Q + IAR + R   +++ DEPT  +     
Sbjct: 122 VAAAMGIEVNLRAR-------VSDLSVADRQMIAIARAMARAPKVLILDEPTSSLSATEA 174

Query: 442 SDIYRLFAELAAQGKGLLVVSSDLRELMQICDRIAVMSAGRIADTFSRDDWSQERILAAA 501
             ++ L   L AQG  +L +S  + ++ +I DRI VM  G I+  F  +       L AA
Sbjct: 175 DRLFELIDRLRAQGVAILYISHRMSDIRRIADRIVVMRDGMISGVFETEPLD----LEAA 230

Query: 502 FSGYVGRQEAAAAAHVAGNT 521
            +  +G +     A V   T
Sbjct: 231 VTAMLGHRMTEVDAEVRQGT 250



 Score = 75.1 bits (183), Expect = 6e-18
 Identities = 60/203 (29%), Positives = 100/203 (49%), Gaps = 6/203 (2%)

Query: 31  IDLDLRPGQVLALTGENGAGKSTLSKIICGLVDASAGGMMLDGQPYAPASRTQAEGLGIR 90
           I L    G+V+AL G  G+GKS L++I+ G+     G + + G+ Y+P S   A   G+ 
Sbjct: 268 ITLTAHDGEVVALVGLLGSGKSRLAEILFGIARPIRGSIRIKGKDYSPRSVKDAIAQGVF 327

Query: 91  MVMQELN---LIPTLSIAENLFLEKLPRRF--GWIDRKKLAEAARAQMEVVGLGELDPWT 145
           M  ++     +IP   IA+N+ L  L       ++  ++    A+  ++ +G+       
Sbjct: 328 MSPKDRGTNAVIPAFDIADNMTLPFLQGMSVGSFLKSRQQRGTAQGMVDRLGIVCQSVRD 387

Query: 146 PVGDLGLGHQQMVEIARNLIGSCRCLILDEPTAMLTNREVELLFSRIERLRAEGVAIIYI 205
            +G L  G+QQ V IAR L+   + L+LDEP   +       +   I R   +G A +  
Sbjct: 388 GIGTLSGGNQQKVMIARWLLEPAQVLLLDEPFQGVDIGARRDIGHHI-RATTQGRATLVF 446

Query: 206 SHRLEELKRIADRIVVLRDGKLV 228
              ++E   IADRIVV+ +G +V
Sbjct: 447 LAEIDEALEIADRIVVMSEGAIV 469


Lambda     K      H
   0.320    0.137    0.390 

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: 643
Number of extensions: 28
Number of successful extensions: 10
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 3
Length of query: 522
Length of database: 498
Length adjustment: 34
Effective length of query: 488
Effective length of database: 464
Effective search space:   226432
Effective search space used:   226432
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: 52 (24.6 bits)

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

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

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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