Alignments for a candidate for PS417_11890 in Dinoroseobacter shibae DFL-12

GapMind for catabolism of small carbon sources

Alignments for a candidate for PS417_11890 in Dinoroseobacter shibae DFL-12

Align Inositol transport system ATP-binding protein (characterized)
to candidate 3609044 Dshi_2433 ABC transporter related (RefSeq)

Query= reanno::WCS417:GFF2332
         (517 letters)



>FitnessBrowser__Dino:3609044
          Length = 510

 Score =  420 bits (1079), Expect = e-122
 Identities = 210/490 (42%), Positives = 320/490 (65%)

Query: 24  LEIVNISKGFPGVVALADVQLRVRPGTVLALMGENGAGKSTLMKIIAGIYQPDAGEIRLR 83
           L + +I+K FPGV AL+DV L + PG V AL+GENGAGKST++KI+ GIYQPD G I + 
Sbjct: 21  LALAHITKTFPGVKALSDVSLSLYPGKVTALIGENGAGKSTVVKILTGIYQPDGGRILVD 80

Query: 84  GKPIVFETPLAAQKAGIAMIHQELNLMPHMSIAENIWIGREQLNSLHMVNHREMHRCTAE 143
           G+P+ F TP AA   G+  IHQE  L   +S+AENI++G     +  +++ ++       
Sbjct: 81  GQPVPFSTPQAAADHGVTAIHQETVLFDELSVAENIFLGHAPRGAFGLIDWKKTTENARA 140

Query: 144 LLARLRINLDPEEQVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITEKEVAHLFSII 203
           LL  +   LDP+ ++ +L IA + +V IA+A+S ++ ++IMDEPT+A++ KE+  L+ ++
Sbjct: 141 LLTSIGAELDPDHKLKDLGIANKHLVAIARALSIEARVVIMDEPTAALSHKEIEELYELV 200

Query: 204 ADLKSQGKGIVYITHKMNEVFAIADEVAVFRDGHYIGLQRADSMNSDSLISMMVGRELSQ 263
             LK+QGK I++I+HK +E+F IAD   VFRDG  IG      +    L+ MMVGR++SQ
Sbjct: 201 ESLKAQGKAILFISHKFDEIFRIADNYTVFRDGQLIGDGAIADVTEADLVKMMVGRDVSQ 260

Query: 264 LFPLRETPIGDLLLTVRDLTLDGVFKDVSFDLHAGEILGIAGLMGSGRTNVAETIFGITP 323
           +FP R   +GD +LTV+       F D+SF L  GEILG  GL+G+GR+   +++FGIT 
Sbjct: 261 IFPQRAPNVGDTVLTVQGYAHPTEFDDISFTLREGEILGFYGLVGAGRSEFMQSLFGITR 320

Query: 324 SSSGQITLDGKAVRISDPHMAIEKGFALLTEDRKLSGLFPCLSVLENMEMAVLPHYTGNG 383
            S+G + + G    IS P  A++ G   + EDR   G    L + +N+ +  L   +  G
Sbjct: 321 PSAGSVEIGGARAEISSPADAVDHGIVYVPEDRGKQGAILDLPIFQNVTLPSLGRISRKG 380

Query: 384 FIQQKALRALCEDMCKKLRVKTPSLEQCIDTLSGGNQQKALLARWLMTNPRLLILDEPTR 443
           F++     AL  +  ++L ++  SL+  +  LSGGNQQK ++A+WL T PR++ILDEPT+
Sbjct: 381 FLRLAEEFALAREYTERLDLRAASLDTHVGNLSGGNQQKVVIAKWLATRPRVIILDEPTK 440

Query: 444 GIDVGAKAEIYRLIAFLASEGMAVIMISSELPEVLGMSDRVMVMHEGELMGTLDRSEATQ 503
           G+D+G+KA ++  +A LA++G+AVIM+SSE+PEVLGMSDRV+VM EG ++  L   +   
Sbjct: 441 GVDIGSKAAVHDFMAELAAQGLAVIMVSSEIPEVLGMSDRVIVMREGRIVAELAGDDLQP 500

Query: 504 EKVMQLASGM 513
           E +++ A+G+
Sbjct: 501 ETLVRHAAGI 510



 Score = 87.4 bits (215), Expect = 1e-21
 Identities = 65/248 (26%), Positives = 117/248 (47%), Gaps = 15/248 (6%)

Query: 21  PYLLEIVNISKGFPGVVALADVQLRVRPGTVLALMGENGAGKSTLMKIIAGIYQPDAGEI 80
           P + + V   +G+       D+   +R G +L   G  GAG+S  M+ + GI +P AG +
Sbjct: 267 PNVGDTVLTVQGYAHPTEFDDISFTLREGEILGFYGLVGAGRSEFMQSLFGITRPSAGSV 326

Query: 81  RLRGKPIVFETPLAAQKAGIAMIHQE---LNLMPHMSIAENIWIGREQLNSLHMVNHREM 137
            + G      +P  A   GI  + ++      +  + I +N+      L SL  ++ +  
Sbjct: 327 EIGGARAEISSPADAVDHGIVYVPEDRGKQGAILDLPIFQNV-----TLPSLGRISRKGF 381

Query: 138 HRCTAEL-LAR---LRINL---DPEEQVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSA 190
            R   E  LAR    R++L     +  VGNLS   +Q V IAK ++    ++I+DEPT  
Sbjct: 382 LRLAEEFALAREYTERLDLRAASLDTHVGNLSGGNQQKVVIAKWLATRPRVIILDEPTKG 441

Query: 191 ITEKEVAHLFSIIADLKSQGKGIVYITHKMNEVFAIADEVAVFRDGHYIGLQRADSMNSD 250
           +     A +   +A+L +QG  ++ ++ ++ EV  ++D V V R+G  +     D +  +
Sbjct: 442 VDIGSKAAVHDFMAELAAQGLAVIMVSSEIPEVLGMSDRVIVMREGRIVAELAGDDLQPE 501

Query: 251 SLISMMVG 258
           +L+    G
Sbjct: 502 TLVRHAAG 509


Lambda     K      H
   0.320    0.136    0.381 

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: 610
Number of extensions: 27
Number of successful extensions: 5
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: 517
Length of database: 510
Length adjustment: 35
Effective length of query: 482
Effective length of database: 475
Effective search space:   228950
Effective search space used:   228950
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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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
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