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

GapMind for catabolism of small carbon sources

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

Align ABC-type sugar transport system, ATP-binding protein; EC 3.6.3.17 (characterized, see rationale)
to candidate 3607108 Dshi_0530 ABC transporter related (RefSeq)

Query= uniprot:A0A0C4Y5F6
         (540 letters)



>FitnessBrowser__Dino:3607108
          Length = 498

 Score =  308 bits (788), Expect = 4e-88
 Identities = 193/494 (39%), Positives = 281/494 (56%), Gaps = 18/494 (3%)

Query: 1   MSDMSDTSTKAPLLALRNICKTFPGVRALRKVELTAYAGEVHALMGENGAGKSTLMKILS 60
           MS   DT+     + LR I K + GV AL  V+ T   GE   L GENG+GKSTL+KI+S
Sbjct: 1   MSSDHDTA----FIDLRAITKRYAGVTALDSVDFTVQPGEAVCLAGENGSGKSTLIKIIS 56

Query: 61  GAYTADPGGECHIDGQRVQIDGPQSARDLGVAVIYQELSLAPNLSVAENIYLGRALQRRG 120
           G   A   G   I GQ      P+ +   GV VI+Q+ SL PNLSVAENI     L  R 
Sbjct: 57  GVEPAT-AGTVQIAGQEHVTLNPRISAAAGVMVIFQDFSLFPNLSVAENIAFTTQLSTRQ 115

Query: 121 LVARGDMVRACA-PTLARLGADFSPAANVASLSIAQRQLVEIARAVHFEARILVMDEPTT 179
            + +   VR  A   L R+G      A V +L +AQ+QLV I RA+  +A++++MDEPTT
Sbjct: 116 RLFKFRAVRDIARAALDRIGVQIDLDARVETLPVAQKQLVAICRALASKAQLIIMDEPTT 175

Query: 180 PLSTHETDRLFALIRQLRGEGMAILYISHRMAEIDELADRVTVLRDGCFVGTLDRAHLSQ 239
            L+  E  RL  +IR L+ EG+A++++SH++AE+ E++++V VLR+G  V     +    
Sbjct: 176 ALTEKEVRRLQGIIRMLKEEGVAVIFVSHKLAEVLEVSEKVVVLRNGKKVAEGPASEFDT 235

Query: 240 AALVKMMVGRDLSGFYTKTHGQAVEREVMLSVRDVADGRRVKGCSFDLRAGEVLGLAGLV 299
            +L   M GRD+          A   + ++ V+ +         SFDLR GEVLG+ GL+
Sbjct: 236 QSLTYHMTGRDVPE--VPPSDVAAGAQTLMQVQGLGKAGSFSDISFDLRTGEVLGITGLL 293

Query: 300 GAGRTELARLVFGADARTRGEVRIANPAGSGGLVTLPAGGPRQAIDAGIAYLTEDRKLQG 359
           G GRT +A+ +FG      G + +           +P G P+ A  A I Y+ EDR  +G
Sbjct: 294 GCGRTSVAKALFGLVTPDAGSILVDGSP-------VPLGDPQAASLARIGYVPEDRLTEG 346

Query: 360 LFLDQSVHENINLIVAARDA-LGLGRLNRTAARRRTTEAIDTLGIRVAHAQVNVGALSGG 418
           LFL QS+  N+   V   DA    G L+ T   +  ++ +  L ++    +  V +LSGG
Sbjct: 347 LFLSQSILRNV--AVGRLDAHTSGGFLDMTGLAKEASDWLRRLKVKAPDVEAPVQSLSGG 404

Query: 419 NQQKVMLSRLLEIQPRVLILDEPTRGVDIGAKSEIYRLINALAQSGVAILMISSELPEVV 478
           NQQ+V L+R L   PRVLIL+ P+ GVD+G+K++I+ +I  LA+ G+ +++IS +LPE++
Sbjct: 405 NQQRVALARWLSRAPRVLILNGPSVGVDVGSKADIHDIIRELAREGIGVIVISDDLPELL 464

Query: 479 GLCDRVLVMREGTL 492
             C RVLVMREG +
Sbjct: 465 ATCHRVLVMREGRI 478



 Score = 80.5 bits (197), Expect = 1e-19
 Identities = 64/213 (30%), Positives = 108/213 (50%), Gaps = 17/213 (7%)

Query: 285 FDLRAGEVLGLAGLVGAGRTELARLVFGADARTRGEVRIANPAGSGGLVTLPAGGPRQAI 344
           F ++ GE + LAG  G+G++ L +++ G +  T G V+IA        VTL    PR + 
Sbjct: 30  FTVQPGEAVCLAGENGSGKSTLIKIISGVEPATAGTVQIAGQEH----VTL---NPRISA 82

Query: 345 DAGIAYLTEDRKLQGLFLDQSVHENINLI--VAARDALGLGRLNRTAARRRTTEAIDTLG 402
            AG+  + +D  L   F + SV ENI     ++ R  L   R  R  AR     A+D +G
Sbjct: 83  AAGVMVIFQDFSL---FPNLSVAENIAFTTQLSTRQRLFKFRAVRDIARA----ALDRIG 135

Query: 403 IRVAHAQVNVGALSGGNQQKVMLSRLLEIQPRVLILDEPTRGVDIGAKSEIYRLINALAQ 462
           +++      V  L    +Q V + R L  + +++I+DEPT  +       +  +I  L +
Sbjct: 136 VQI-DLDARVETLPVAQKQLVAICRALASKAQLIIMDEPTTALTEKEVRRLQGIIRMLKE 194

Query: 463 SGVAILMISSELPEVVGLCDRVLVMREGTLAGE 495
            GVA++ +S +L EV+ + ++V+V+R G    E
Sbjct: 195 EGVAVIFVSHKLAEVLEVSEKVVVLRNGKKVAE 227



 Score = 68.2 bits (165), Expect = 7e-16
 Identities = 55/207 (26%), Positives = 98/207 (47%), Gaps = 7/207 (3%)

Query: 39  GEVHALMGENGAGKSTLMKILSGAYTADPGGECHIDGQRVQIDGPQSARDLGVAVIYQEL 98
           GEV  + G  G G++++ K L G  T D  G   +DG  V +  PQ+A    +  + ++ 
Sbjct: 284 GEVLGITGLLGCGRTSVAKALFGLVTPD-AGSILVDGSPVPLGDPQAASLARIGYVPEDR 342

Query: 99  ---SLAPNLSVAENIYLGR--ALQRRGLVARGDMVRACAPTLARLGADFSPA-ANVASLS 152
               L  + S+  N+ +GR  A    G +    + +  +  L RL        A V SLS
Sbjct: 343 LTEGLFLSQSILRNVAVGRLDAHTSGGFLDMTGLAKEASDWLRRLKVKAPDVEAPVQSLS 402

Query: 153 IAQRQLVEIARAVHFEARILVMDEPTTPLSTHETDRLFALIRQLRGEGMAILYISHRMAE 212
              +Q V +AR +    R+L+++ P+  +       +  +IR+L  EG+ ++ IS  + E
Sbjct: 403 GGNQQRVALARWLSRAPRVLILNGPSVGVDVGSKADIHDIIRELAREGIGVIVISDDLPE 462

Query: 213 IDELADRVTVLRDGCFVGTLDRAHLSQ 239
           +     RV V+R+G  +  L+   L++
Sbjct: 463 LLATCHRVLVMREGRIIDALEGTALTE 489


Lambda     K      H
   0.320    0.136    0.382 

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: 588
Number of extensions: 30
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: 540
Length of database: 498
Length adjustment: 35
Effective length of query: 505
Effective length of database: 463
Effective search space:   233815
Effective search space used:   233815
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