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 3609577 Dshi_2961 ABC transporter related (RefSeq)

Query= uniprot:D8IUD1
         (522 letters)



>FitnessBrowser__Dino:3609577
          Length = 511

 Score =  271 bits (693), Expect = 4e-77
 Identities = 183/487 (37%), Positives = 263/487 (54%), Gaps = 30/487 (6%)

Query: 13  LLTLSGIGKRYAAPVL-DGIDLDLRPGQVLALTGENGAGKSTLSKIICGLVDASAGGMML 71
           LL ++G+ K Y   V  D +  ++  G+V AL GENGAGKSTL K+I GLV   +G M  
Sbjct: 4   LLRVAGLTKAYPGVVANDDVSFEIAEGEVHALLGENGAGKSTLVKMIYGLVRPDSGTMTF 63

Query: 72  DGQPYAPASRTQAEGLGIRMVMQELNLIPTLSIAENLFLEKLPRRFGWIDRKKLAEAARA 131
            G P+AP     A   G+ MV Q  +L   L++AEN+ L       G  D  K+ + A  
Sbjct: 64  GGVPFAPPEPRAARSAGVAMVFQHFSLFEALTVAENIAL-------GMEDPPKMRDLAAR 116

Query: 132 QMEV---VGLGELDPWTPVGDLGLGHQQMVEIARNLIGSCRCLILDEPTAMLTNREVELL 188
             +V    GL  LDP   VG L  G +Q VEI R L+   + LI+DEPT++LT +EV++L
Sbjct: 117 ITQVSQAYGL-PLDPSRLVGTLSAGERQRVEIIRCLLQEPKLLIMDEPTSVLTPQEVDIL 175

Query: 189 FSRIERLRAEGVAIIYISHRLEELKRIADRIVVLRDGKLVCNDDIGRYSTEQLVQLMAGE 248
           F+ + +LR EG AI+YISH+LEE++ + D   +LR GK+V   D    S  +L ++M G+
Sbjct: 176 FATLRKLRDEGTAILYISHKLEEIRALCDSATILRLGKVVATCDPREKSARELAEMMVGK 235

Query: 249 LTKVDLDAEHRRIGAPVLRIRGLGRAPVVHP-------ASLALHAGEVLGIAGLIGSGRT 301
            T     +     GAPVL +RGL + P   P        SL + AGEVLGI G+ G+G+ 
Sbjct: 236 -TLQQTKSAGNAFGAPVLELRGLSQ-PATTPFGTPLRDISLEVRAGEVLGIGGVAGNGQD 293

Query: 302 ELLRLIFGADRAEQGEIFIGDSQEPARIRSPKDAVKAGIAMVTEDRKGQGLLLPQAISVN 361
           ELL  I G  RAE      G    P     P    + G+    E+R G       +++ N
Sbjct: 294 ELLSAISGERRAEDAIFLHG---TPISKIGPAARRQLGVLSGPEERLGHAAAPDMSLTEN 350

Query: 362 TSLANLGSV----SRGGMLDHAAESSVAQDYVKKLRIRSGSVAQAAGELSGGNQQKVVIA 417
             L   GSV    +R G LD A   + A+  ++   +R+     AA  LSGGN QK VI 
Sbjct: 351 ALLT--GSVREKLTRNGFLDWAKTRAFAERIIETFDVRTPGPEAAARALSGGNLQKFVIG 408

Query: 418 RWLYRDCPIMLFDEPTRGIDIGAKSDIYRLFAELAAQGKGLLVVSSDLRELMQICDRIAV 477
           R + +   +++ ++PT G+D  A + I +   +LAA G  ++V+S DL ELM+I D  A 
Sbjct: 409 REVLQRPEVLIVNQPTWGVDASAAAAIRQALLDLAAGGTAVVVISQDLDELMEISDTFAA 468

Query: 478 MSAGRIA 484
           ++ GR++
Sbjct: 469 LNGGRLS 475



 Score = 77.4 bits (189), Expect = 1e-18
 Identities = 66/227 (29%), Positives = 111/227 (48%), Gaps = 18/227 (7%)

Query: 265 VLRIRGLGRA-PVV---HPASLALHAGEVLGIAGLIGSGRTELLRLIFGADRAEQGEIFI 320
           +LR+ GL +A P V      S  +  GEV  + G  G+G++ L+++I+G  R + G +  
Sbjct: 4   LLRVAGLTKAYPGVVANDDVSFEIAEGEVHALLGENGAGKSTLVKMIYGLVRPDSGTMTF 63

Query: 321 GDSQEPARIRSPKDAVKAGIAMVTEDRKGQGLLLPQAISVNTSLANLGSVSRGGMLDHAA 380
           G    P     P+ A  AG+AMV      Q   L +A++V  ++A LG      M D AA
Sbjct: 64  GGV--PFAPPEPRAARSAGVAMVF-----QHFSLFEALTVAENIA-LGMEDPPKMRDLAA 115

Query: 381 E-SSVAQDYVKKLRIRSGSVAQAAGELSGGNQQKVVIARWLYRDCPIMLFDEPTRGIDIG 439
             + V+Q Y   L       ++  G LS G +Q+V I R L ++  +++ DEPT  +   
Sbjct: 116 RITQVSQAYGLPL-----DPSRLVGTLSAGERQRVEIIRCLLQEPKLLIMDEPTSVLTPQ 170

Query: 440 AKSDIYRLFAELAAQGKGLLVVSSDLRELMQICDRIAVMSAGRIADT 486
               ++    +L  +G  +L +S  L E+  +CD   ++  G++  T
Sbjct: 171 EVDILFATLRKLRDEGTAILYISHKLEEIRALCDSATILRLGKVVAT 217



 Score = 70.5 bits (171), Expect = 1e-16
 Identities = 75/259 (28%), Positives = 112/259 (43%), Gaps = 20/259 (7%)

Query: 10  GSPLLTLSGIGKRYAAPV---LDGIDLDLRPGQVLALTGENGAGKSTLSKIICGLVDASA 66
           G+P+L L G+ +    P    L  I L++R G+VL + G  G G+  L   I G   A  
Sbjct: 248 GAPVLELRGLSQPATTPFGTPLRDISLEVRAGEVLGIGGVAGNGQDELLSAISGERRAE- 306

Query: 67  GGMMLDGQPYA---PASRTQAEGLGIRMVMQEL---NLIPTLSIAENLFL-----EKLPR 115
             + L G P +   PA+R Q   LG+    +E       P +S+ EN  L     EKL R
Sbjct: 307 DAIFLHGTPISKIGPAARRQ---LGVLSGPEERLGHAAAPDMSLTENALLTGSVREKLTR 363

Query: 116 RFGWIDRKKLAEAARAQMEVVGLGELDPWTPVGDLGLGHQQMVEIARNLIGSCRCLILDE 175
             G++D  K    A   +E   +    P      L  G+ Q   I R ++     LI+++
Sbjct: 364 N-GFLDWAKTRAFAERIIETFDVRTPGPEAAARALSGGNLQKFVIGREVLQRPEVLIVNQ 422

Query: 176 PTAMLTNREVELLFSRIERLRAEGVAIIYISHRLEELKRIADRIVVLRDGKLVCNDDIGR 235
           PT  +       +   +  L A G A++ IS  L+EL  I+D    L  G+L        
Sbjct: 423 PTWGVDASAAAAIRQALLDLAAGGTAVVVISQDLDELMEISDTFAALNGGRLSGKVPAAG 482

Query: 236 YSTEQLVQLMAGELTKVDL 254
            + EQ + LM G    +DL
Sbjct: 483 LTVEQ-IGLMLGGAHDMDL 500


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: 644
Number of extensions: 47
Number of successful extensions: 8
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: 511
Length adjustment: 35
Effective length of query: 487
Effective length of database: 476
Effective search space:   231812
Effective search space used:   231812
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