GapMind for catabolism of small carbon sources

 

Alignments 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 3607108 Dshi_0530 ABC transporter related (RefSeq)

Query= uniprot:B2SYR5
         (512 letters)



>FitnessBrowser__Dino:3607108
          Length = 498

 Score =  287 bits (735), Expect = 5e-82
 Identities = 166/481 (34%), Positives = 270/481 (56%), Gaps = 4/481 (0%)

Query: 10  IGKVFPGVRALDGVSFDVNVGQVHGLMGENGAGKSTLLKILGGEYQPDSGRVMIDGNEVR 69
           I K + GV ALD V F V  G+   L GENG+GKSTL+KI+ G     +G V I G E  
Sbjct: 15  ITKRYAGVTALDSVDFTVQPGEAVCLAGENGSGKSTLIKIISGVEPATAGTVQIAGQEHV 74

Query: 70  FTSAASSIAAGIAVIHQELQYVPDLTVAENLLLG-QLPNSLGWVNKREAKRFVRERLEAM 128
             +   S AAG+ VI Q+    P+L+VAEN+    QL         R  +   R  L+ +
Sbjct: 75  TLNPRISAAAGVMVIFQDFSLFPNLSVAENIAFTTQLSTRQRLFKFRAVRDIARAALDRI 134

Query: 129 GVALDPNAKLRKLSIAQRQMVEICKALLRNARVIALDEPTSSLSHRETEVLFKLVRDLRA 188
           GV +D +A++  L +AQ+Q+V IC+AL   A++I +DEPT++L+ +E   L  ++R L+ 
Sbjct: 135 GVQIDLDARVETLPVAQKQLVAICRALASKAQLIIMDEPTTALTEKEVRRLQGIIRMLKE 194

Query: 189 DNRAMIYISHRMDEIYELCDACTIFRDGRKIASHPTLEGVTRDTIVSEMVGREISDIYNY 248
           +  A+I++SH++ E+ E+ +   + R+G+K+A  P  E  T+ ++   M GR++ ++   
Sbjct: 195 EGVAVIFVSHKLAEVLEVSEKVVVLRNGKKVAEGPASEFDTQ-SLTYHMTGRDVPEVPPS 253

Query: 249 SARPLGEVRFAAKGIEGHALAQPASFEVRRGEIVGFFGLVGAGRSELMHLVYGADHKKGG 308
                 +     +G+         SF++R GE++G  GL+G GR+ +   ++G      G
Sbjct: 254 DVAAGAQTLMQVQGLGKAGSFSDISFDLRTGEVLGITGLLGCGRTSVAKALFGLVTPDAG 313

Query: 309 ELLLDGKPIKVRSAGEAIRHGIVLCPEDRKEEGIVAMATVSENINISCRRHYLRVGMFLD 368
            +L+DG P+ +     A    I   PEDR  EG+    ++  N+ +  R      G FLD
Sbjct: 314 SILVDGSPVPLGDPQAASLARIGYVPEDRLTEGLFLSQSILRNVAVG-RLDAHTSGGFLD 372

Query: 369 RKKEAETADRFIKLLKIKTPSRRQKIRFLSGGNQQKAILSRWLAEPDLKVVILDEPTRGI 428
               A+ A  +++ LK+K P     ++ LSGGNQQ+  L+RWL+    +V+IL+ P+ G+
Sbjct: 373 MTGLAKEASDWLRRLKVKAPDVEAPVQSLSGGNQQRVALARWLSRAP-RVLILNGPSVGV 431

Query: 429 DVGAKHEIYNVIYQLAERGCAIVMISSELPEVLGVSDRIVVMRQGRISGELTRKDATEQS 488
           DVG+K +I+++I +LA  G  +++IS +LPE+L    R++VMR+GRI   L     TE  
Sbjct: 432 DVGSKADIHDIIRELAREGIGVIVISDDLPELLATCHRVLVMREGRIIDALEGTALTEDD 491

Query: 489 V 489
           +
Sbjct: 492 L 492



 Score = 64.7 bits (156), Expect = 7e-15
 Identities = 60/258 (23%), Positives = 112/258 (43%), Gaps = 15/258 (5%)

Query: 255 EVRFAAKGIEGHALAQPASFEVRRGEIVGFFGLVGAGRSELMHLVYGADHKKGGELLLDG 314
           ++R   K   G        F V+ GE V   G  G+G+S L+ ++ G +    G + + G
Sbjct: 11  DLRAITKRYAGVTALDSVDFTVQPGEAVCLAGENGSGKSTLIKIISGVEPATAGTVQIAG 70

Query: 315 KPIKVRSAGEAIRHGIVLCPEDRKEEGIVAMATVSENI----NISCRRHYLRVGMFLDRK 370
           +     +   +   G+++  +D     +    +V+ENI     +S R+   +     D  
Sbjct: 71  QEHVTLNPRISAAAGVMVIFQDFS---LFPNLSVAENIAFTTQLSTRQRLFKFRAVRDIA 127

Query: 371 KEAETADRFIKLLKIKTPSRRQKIRFLSGGNQQKAILSRWLAEPDLKVVILDEPTRGIDV 430
           + A   DR    + +       ++  L    +Q   + R LA    +++I+DEPT  +  
Sbjct: 128 RAA--LDRIGVQIDLDA-----RVETLPVAQKQLVAICRALASK-AQLIIMDEPTTALTE 179

Query: 431 GAKHEIYNVIYQLAERGCAIVMISSELPEVLGVSDRIVVMRQGRISGELTRKDATEQSVL 490
                +  +I  L E G A++ +S +L EVL VS+++VV+R G+   E    +   QS+ 
Sbjct: 180 KEVRRLQGIIRMLKEEGVAVIFVSHKLAEVLEVSEKVVVLRNGKKVAEGPASEFDTQSLT 239

Query: 491 SLALPQSSTALPGTQAAA 508
                +    +P +  AA
Sbjct: 240 YHMTGRDVPEVPPSDVAA 257


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: 578
Number of extensions: 31
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: 512
Length of database: 498
Length adjustment: 34
Effective length of query: 478
Effective length of database: 464
Effective search space:   221792
Effective search space used:   221792
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:

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:

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:

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:

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