Aligments for a candidate for BPHYT_RS16930 in Dinoroseobacter shibae DFL-12

GapMind for catabolism of small carbon sources

Aligments for a candidate for BPHYT_RS16930 in Dinoroseobacter shibae DFL-12

Align Arabinose import ATP-binding protein AraG; EC 7.5.2.12 (characterized, see rationale)
to candidate 3609044 Dshi_2433 ABC transporter related (RefSeq)

Query= uniprot:B2SYR5
         (512 letters)



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

 Score =  376 bits (966), Expect = e-109
 Identities = 198/489 (40%), Positives = 305/489 (62%), Gaps = 4/489 (0%)

Query: 3   ATLRFDNIGKVFPGVRALDGVSFDVNVGQVHGLMGENGAGKSTLLKILGGEYQPDSGRVM 62
           A L   +I K FPGV+AL  VS  +  G+V  L+GENGAGKST++KIL G YQPD GR++
Sbjct: 19  AALALAHITKTFPGVKALSDVSLSLYPGKVTALIGENGAGKSTVVKILTGIYQPDGGRIL 78

Query: 63  IDGNEVRFTSAASSIAAGIAVIHQELQYVPDLTVAENLLLGQLP-NSLGWVNKREAKRFV 121
           +DG  V F++  ++   G+  IHQE     +L+VAEN+ LG  P  + G ++ ++     
Sbjct: 79  VDGQPVPFSTPQAAADHGVTAIHQETVLFDELSVAENIFLGHAPRGAFGLIDWKKTTENA 138

Query: 122 RERLEAMGVALDPNAKLRKLSIAQRQMVEICKALLRNARVIALDEPTSSLSHRETEVLFK 181
           R  L ++G  LDP+ KL+ L IA + +V I +AL   ARV+ +DEPT++LSH+E E L++
Sbjct: 139 RALLTSIGAELDPDHKLKDLGIANKHLVAIARALSIEARVVIMDEPTAALSHKEIEELYE 198

Query: 182 LVRDLRADNRAMIYISHRMDEIYELCDACTIFRDGRKIASHPTLEGVTRDTIVSEMVGRE 241
           LV  L+A  +A+++ISH+ DEI+ + D  T+FRDG+ I     +  VT   +V  MVGR+
Sbjct: 199 LVESLKAQGKAILFISHKFDEIFRIADNYTVFRDGQLIGD-GAIADVTEADLVKMMVGRD 257

Query: 242 ISDIYNYSARPLGEVRFAAKGIEGHALAQPASFEVRRGEIVGFFGLVGAGRSELMHLVYG 301
           +S I+   A  +G+     +G          SF +R GEI+GF+GLVGAGRSE M  ++G
Sbjct: 258 VSQIFPQRAPNVGDTVLTVQGYAHPTEFDDISFTLREGEILGFYGLVGAGRSEFMQSLFG 317

Query: 302 ADHKKGGELLLDGKPIKVRSAGEAIRHGIVLCPEDRKEEGIVAMATVSENINISCRRHYL 361
                 G + + G   ++ S  +A+ HGIV  PEDR ++G +    + +N+ +       
Sbjct: 318 ITRPSAGSVEIGGARAEISSPADAVDHGIVYVPEDRGKQGAILDLPIFQNVTLPSLGRIS 377

Query: 362 RVGMFLDRKKEAETADRFIKLLKIKTPSRRQKIRFLSGGNQQKAILSRWLAEPDLKVVIL 421
           R G FL   +E   A  + + L ++  S    +  LSGGNQQK ++++WLA    +V+IL
Sbjct: 378 RKG-FLRLAEEFALAREYTERLDLRAASLDTHVGNLSGGNQQKVVIAKWLATRP-RVIIL 435

Query: 422 DEPTRGIDVGAKHEIYNVIYQLAERGCAIVMISSELPEVLGVSDRIVVMRQGRISGELTR 481
           DEPT+G+D+G+K  +++ + +LA +G A++M+SSE+PEVLG+SDR++VMR+GRI  EL  
Sbjct: 436 DEPTKGVDIGSKAAVHDFMAELAAQGLAVIMVSSEIPEVLGMSDRVIVMREGRIVAELAG 495

Query: 482 KDATEQSVL 490
            D   ++++
Sbjct: 496 DDLQPETLV 504



 Score = 80.9 bits (198), Expect = 1e-19
 Identities = 62/234 (26%), Positives = 110/234 (47%), Gaps = 11/234 (4%)

Query: 261 KGIEGHALAQPASFEVRRGEIVGFFGLVGAGRSELMHLVYGADHKKGGELLLDGKPIKVR 320
           K   G       S  +  G++    G  GAG+S ++ ++ G     GG +L+DG+P+   
Sbjct: 28  KTFPGVKALSDVSLSLYPGKVTALIGENGAGKSTVVKILTGIYQPDGGRILVDGQPVPFS 87

Query: 321 SAGEAIRHGIVLCPEDRKEEGIVAMATVSENINISCRRHYLRVGMF--LDRKKEAETADR 378
           +   A  HG+       +E  +    +V+ENI +    H  R G F  +D KK  E A  
Sbjct: 88  TPQAAADHGVTAI---HQETVLFDELSVAENIFLG---HAPR-GAFGLIDWKKTTENARA 140

Query: 379 FIKLLKIKTPSRRQKIRFLSGGNQQKAILSRWLAEPDLKVVILDEPTRGIDVGAKHEIYN 438
            +  +  +      K++ L   N+    ++R L+  + +VVI+DEPT  +      E+Y 
Sbjct: 141 LLTSIGAELDPDH-KLKDLGIANKHLVAIARALSI-EARVVIMDEPTAALSHKEIEELYE 198

Query: 439 VIYQLAERGCAIVMISSELPEVLGVSDRIVVMRQGRISGELTRKDATEQSVLSL 492
           ++  L  +G AI+ IS +  E+  ++D   V R G++ G+    D TE  ++ +
Sbjct: 199 LVESLKAQGKAILFISHKFDEIFRIADNYTVFRDGQLIGDGAIADVTEADLVKM 252


Lambda     K      H
   0.320    0.136    0.385 

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: 673
Number of extensions: 38
Number of successful extensions: 9
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: 512
Length of database: 510
Length adjustment: 35
Effective length of query: 477
Effective length of database: 475
Effective search space:   226575
Effective search space used:   226575
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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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 preprint 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