Alignments for a candidate for araG in Paraburkholderia bryophila 376MFSha3.1

GapMind for catabolism of small carbon sources

Alignments for a candidate for araG in Paraburkholderia bryophila 376MFSha3.1

Align L-arabinose ABC transporter, ATP-binding protein AraG; EC 3.6.3.17 (characterized)
to candidate H281DRAFT_06298 H281DRAFT_06298 L-arabinose ABC transporter ATP-binding protein

Query= CharProtDB::CH_014279
         (504 letters)



>FitnessBrowser__Burk376:H281DRAFT_06298
          Length = 519

 Score =  514 bits (1325), Expect = e-150
 Identities = 265/497 (53%), Positives = 351/497 (70%), Gaps = 1/497 (0%)

Query: 8   LSFRGIGKTFPGVKALTDISFDCYAGQVHALMGENGAGKSTLLKILSGNYAPTTGSVVIN 67
           L F  IGK FPGV+AL  +SFD   GQVH LMGENGAGKSTLLKIL G Y P +G V+I+
Sbjct: 12  LRFDNIGKVFPGVRALDGVSFDVNVGQVHGLMGENGAGKSTLLKILGGEYQPDSGRVMID 71

Query: 68  GQEMSFSDTTAALNAGVAIIYQELHLVPEMTVAENIYLGQLPHKGGIVNRSLLNYEAGLQ 127
           G+E+ F+   +++ AG+A+I+QEL  VP++TVAEN+ LGQLP+  G VN+         +
Sbjct: 72  GKEVRFTSAASSIAAGIAVIHQELQYVPDLTVAENLLLGQLPNSFGWVNKRDAKRFVRER 131

Query: 128 LKHLGMDIDPDTPLKYLSIGQWQMVEIAKALARNAKIIAFDEPTSSLSAREIDNLFRVIR 187
           L+ +G+ +DP+  L+ LSI Q QMVEI KAL RNA++IA DEPTSSLS RE + LF+++R
Sbjct: 132 LEAMGVALDPNAKLRKLSIAQRQMVEICKALLRNARVIALDEPTSSLSHRETEVLFKLVR 191

Query: 188 ELRKEGRVILYVSHRMEEIFALSDAITVFKDGRYVKTFTDMQQVDHDALVQAMVGRDIGD 247
           +LR + R ++Y+SHRM+EI+ L DA T+F+DGR + +   ++ V  D +V  MVGR+I D
Sbjct: 192 DLRADNRAMIYISHRMDEIYELCDACTIFRDGRKIASHPTLEGVSRDTIVSEMVGREISD 251

Query: 248 IYGWQPRSYGEERLRLDAVKAPGVRTPISLAVRSGEIVGLFGLVGAGRSELMKGMFGGTQ 307
           IY +  R  GE R    A++   +  P S  VR GEIVG FGLVGAGRSELM  ++G   
Sbjct: 252 IYNYSERPLGEVRFAAKAIEGHALSQPASFEVRRGEIVGFFGLVGAGRSELMHLVYGTEH 311

Query: 308 ITAGQVYIDQQPIDIRKPSHAIAAGMMLCPEDRKAEGIIPVHSVRDNINISARRKHVLGG 367
              G++ +D + I ++    AI  G++LCPEDRK EGI+ + +V +NINIS RR ++  G
Sbjct: 312 KKGGELVLDGKTIRVKSAGEAIRHGIVLCPEDRKEEGIVAMATVSENINISCRRHYLRAG 371

Query: 368 CVINNGWEENNADHHIRSLNIKTPGAEQLIMNLSGGNQQKAILGRWLSE-EMKVILLDEP 426
             ++   E   AD  I+ L IKTP   Q I  LSGGNQQKAIL RWL+E ++KV++LDEP
Sbjct: 372 VFLDRKKEAETADRFIKLLKIKTPSRRQKIRFLSGGNQQKAILSRWLAEPDLKVVILDEP 431

Query: 427 TRGIDVGAKHEIYNVIYALAAQGVAVLFASSDLPEVLGVADRIVVMREGEIAGELLHEQA 486
           TRGIDVGAKHEIYNVIY LA +G A++  SS+LPEVLGV+DRIVVMR+G IAGEL  + A
Sbjct: 432 TRGIDVGAKHEIYNVIYQLAERGCAIVMISSELPEVLGVSDRIVVMRQGRIAGELSRKDA 491

Query: 487 DERQALSLAMPKVSQAV 503
            E+  LSLA+P+ S A+
Sbjct: 492 TEQAVLSLALPQSSTAL 508



 Score = 68.9 bits (167), Expect = 4e-16
 Identities = 56/223 (25%), Positives = 99/223 (44%), Gaps = 8/223 (3%)

Query: 6   PYLSFRGIGKTFPGVKALTDISFDCYAGQVHALMGENGAGKSTLLKILSGNYAPTTGSVV 65
           P    R   K   G       SF+   G++    G  GAG+S L+ ++ G      G +V
Sbjct: 259 PLGEVRFAAKAIEGHALSQPASFEVRRGEIVGFFGLVGAGRSELMHLVYGTEHKKGGELV 318

Query: 66  INGQEMSFSDTTAALNAGVAII---YQELHLVPEMTVAENIYLGQLPH---KGGIVNRSL 119
           ++G+ +       A+  G+ +     +E  +V   TV+ENI +    H    G  ++R  
Sbjct: 319 LDGKTIRVKSAGEAIRHGIVLCPEDRKEEGIVAMATVSENINISCRRHYLRAGVFLDRKK 378

Query: 120 LNYEAGLQLKHLGMDI-DPDTPLKYLSIGQWQMVEIAKALAR-NAKIIAFDEPTSSLSAR 177
               A   +K L +        +++LS G  Q   +++ LA  + K++  DEPT  +   
Sbjct: 379 EAETADRFIKLLKIKTPSRRQKIRFLSGGNQQKAILSRWLAEPDLKVVILDEPTRGIDVG 438

Query: 178 EIDNLFRVIRELRKEGRVILYVSHRMEEIFALSDAITVFKDGR 220
               ++ VI +L + G  I+ +S  + E+  +SD I V + GR
Sbjct: 439 AKHEIYNVIYQLAERGCAIVMISSELPEVLGVSDRIVVMRQGR 481


Lambda     K      H
   0.319    0.136    0.391 

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: 724
Number of extensions: 30
Number of successful extensions: 7
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: 504
Length of database: 519
Length adjustment: 35
Effective length of query: 469
Effective length of database: 484
Effective search space:   226996
Effective search space used:   226996
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 (21.7 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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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