Aligments for a candidate for BPHYT_RS34245 in Dinoroseobacter shibae DFL-12

GapMind for catabolism of small carbon sources

Aligments for a candidate for BPHYT_RS34245 in Dinoroseobacter shibae DFL-12

Align ABC transporter related; Flags: Precursor (characterized, see rationale)
to candidate 3609044 Dshi_2433 ABC transporter related (RefSeq)

Query= uniprot:B2T9V9
         (510 letters)



>lcl|FitnessBrowser__Dino:3609044 Dshi_2433 ABC transporter related
           (RefSeq)
          Length = 510

 Score =  280 bits (716), Expect = 9e-80
 Identities = 165/472 (34%), Positives = 260/472 (55%), Gaps = 8/472 (1%)

Query: 20  VTKRFGSTAALNDVSIRVMPGESHALVGRNGAGKSTLVSILTGLRKPDTGEVRFSGAAAP 79
           +TK F    AL+DVS+ + PG+  AL+G NGAGKST+V ILTG+ +PD G +   G   P
Sbjct: 26  ITKTFPGVKALSDVSLSLYPGKVTALIGENGAGKSTVVKILTGIYQPDGGRILVDGQPVP 85

Query: 80  SIADRDAWRERVACVYQHSTIIRDLSVAENLFINRQPLRG--GVIDWQAMRRDARALLDH 137
               + A    V  ++Q + +  +LSVAEN+F+   P RG  G+IDW+    +ARALL  
Sbjct: 86  FSTPQAAADHGVTAIHQETVLFDELSVAENIFLGHAP-RGAFGLIDWKKTTENARALLTS 144

Query: 138 WKIDVREDARAGDLSVEARQLVEIARALSYGARFIILDEPTAQLDGDEIKRLFRRISELQ 197
              ++  D +  DL +  + LV IARALS  AR +I+DEPTA L   EI+ L+  +  L+
Sbjct: 145 IGAELDPDHKLKDLGIANKHLVAIARALSIEARVVIMDEPTAALSHKEIEELYELVESLK 204

Query: 198 REGVTFLFISHHLQEVYEICQAVTVLRDARHIVSAPVSALPREQLIEAMTGERGGLAVAD 257
            +G   LFISH   E++ I    TV RD + I    ++ +    L++ M G         
Sbjct: 205 AQGKAILFISHKFDEIFRIADNYTVFRDGQLIGDGAIADVTEADLVKMMVGRDVSQIFPQ 264

Query: 258 AAARGALPADTAVALELKELTGADYEGVSFTVKRGEVVGLTGATSSGRTSVAEAIAGLRA 317
            A       DT + ++       +++ +SFT++ GE++G  G   +GR+   +++ G+  
Sbjct: 265 RAPN---VGDTVLTVQ-GYAHPTEFDDISFTLREGEILGFYGLVGAGRSEFMQSLFGITR 320

Query: 318 AKRGTISVDGAILPPGDVPASLAHGIGCVPKDRHHEGLVLTQSVAENASMTIARVLGKFG 377
              G++ + GA         ++ HGI  VP+DR  +G +L   + +N ++     + + G
Sbjct: 321 PSAGSVEIGGARAEISSPADAVDHGIVYVPEDRGKQGAILDLPIFQNVTLPSLGRISRKG 380

Query: 378 IAAPAKKNAFGQKMIDALGIVAQGPEHVVSGLSGGNQQKVVMARALATNPNVLVLIDPTA 437
               A++ A  ++  + L + A   +  V  LSGGNQQKVV+A+ LAT P V++L +PT 
Sbjct: 381 FLRLAEEFALAREYTERLDLRAASLDTHVGNLSGGNQQKVVIAKWLATRPRVIILDEPTK 440

Query: 438 GVDVKSKEALLSVVDRVREEGKAVLVVSGELDD-LRTCDRVLVMFRGRVAAE 488
           GVD+ SK A+   +  +  +G AV++VS E+ + L   DRV+VM  GR+ AE
Sbjct: 441 GVDIGSKAAVHDFMAELAAQGLAVIMVSSEIPEVLGMSDRVIVMREGRIVAE 492



 Score = 70.1 bits (170), Expect = 2e-16
 Identities = 63/227 (27%), Positives = 102/227 (44%), Gaps = 12/227 (5%)

Query: 31  NDVSIRVMPGESHALVGRNGAGKSTLVSILTGLRKPDTGEVRFSGAAAPSIADRDAWRER 90
           +D+S  +  GE     G  GAG+S  +  L G+ +P  G V   GA A   +  DA    
Sbjct: 286 DDISFTLREGEILGFYGLVGAGRSEFMQSLFGITRPSAGSVEIGGARAEISSPADAVDHG 345

Query: 91  VACVYQH---STIIRDLSVAENLFINRQPLRGGVIDWQAMR-RDARALLDHW--KIDVRE 144
           +  V +       I DL + +N+ +   P  G +     +R  +  AL   +  ++D+R 
Sbjct: 346 IVYVPEDRGKQGAILDLPIFQNVTL---PSLGRISRKGFLRLAEEFALAREYTERLDLRA 402

Query: 145 ---DARAGDLSVEARQLVEIARALSYGARFIILDEPTAQLDGDEIKRLFRRISELQREGV 201
              D   G+LS   +Q V IA+ L+   R IILDEPT  +D      +   ++EL  +G+
Sbjct: 403 ASLDTHVGNLSGGNQQKVVIAKWLATRPRVIILDEPTKGVDIGSKAAVHDFMAELAAQGL 462

Query: 202 TFLFISHHLQEVYEICQAVTVLRDARHIVSAPVSALPREQLIEAMTG 248
             + +S  + EV  +   V V+R+ R +       L  E L+    G
Sbjct: 463 AVIMVSSEIPEVLGMSDRVIVMREGRIVAELAGDDLQPETLVRHAAG 509


Lambda     K      H
   0.318    0.134    0.377 

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: 602
Number of extensions: 33
Number of successful extensions: 8
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 510
Length of database: 510
Length adjustment: 34
Effective length of query: 476
Effective length of database: 476
Effective search space:   226576
Effective search space used:   226576
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 (21.7 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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Steps (tab-delimited)
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Protein sequences (fasta format)
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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, 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