Alignments for a candidate for HSERO_RS05250 in Phaeobacter inhibens BS107

GapMind for catabolism of small carbon sources

Alignments for a candidate for HSERO_RS05250 in Phaeobacter inhibens BS107

Align Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale)
to candidate GFF2770 PGA1_c28130 ABC transporter, ATP-binding protein

Query= uniprot:D8J111
         (520 letters)



>FitnessBrowser__Phaeo:GFF2770
          Length = 505

 Score =  291 bits (746), Expect = 3e-83
 Identities = 175/495 (35%), Positives = 276/495 (55%), Gaps = 16/495 (3%)

Query: 21  PVIALRNVCKRFPGVLALDNCQFELAAGEVHALMGENGAGKSTLMKILSGVYQRDSGDIL 80
           P+++L+ + K +PGV+A D   F++ AGEVHAL+GENGAGKSTL+K++ G+ + DSG +L
Sbjct: 4   PLLSLQGLTKAYPGVVANDTVSFDIGAGEVHALLGENGAGKSTLVKMIYGLVKPDSGKML 63

Query: 81  LDGKPVEITEPRQAQALGIGIIHQELNLMNHLSAAQNIFIGREPRKAMGLFIDEDELNRQ 140
           L G+P    EPRQA+A GI ++ Q  +L + L+ A+NI +G E   A+       +L  Q
Sbjct: 64  LHGEPYTPGEPRQARADGIAMVFQHFSLFDALNVAENIALGMETPPAL------RDLATQ 117

Query: 141 AAAIFARMRLDMDPSTPVGELTVARQQMVEIAKALSFDSRVLIMDEPTAALNNAEIAELF 200
              +     L +DP   VG+L+   +Q VEI + L  D ++LIMDEPT+ L   E+  LF
Sbjct: 118 IRKVSETYGLPLDPYRTVGDLSAGERQRVEIIRCLLQDPKLLIMDEPTSVLTPQEVEILF 177

Query: 201 RIIRDLQAQGVGIVYISHKMDELRQIADRVSVMRDGKYIATVPMQETSMDTIISMMVGRA 260
           + ++ L+++G  I+YISHK++E+R + D  +++R GK +      ETS   +  MMVG A
Sbjct: 178 QTLQKLRSEGTSILYISHKLEEIRTLCDHATILRLGKNVGECVPSETSARDMAEMMVGTA 237

Query: 261 LDGEQRIPPDTSRNDVVLEVRGLN------RGRAIRDVSFTLRKGEILGFAGLMGAGRTE 314
           L   +R     +  DV L++ GL+       G A+++V  T+RKGEILG  G+ G G+ E
Sbjct: 238 LQTPER--SGRALGDVALDISGLSVPAPSAFGTALKNVHMTVRKGEILGVGGVAGNGQDE 295

Query: 315 VARAIFGADPLEAGEIIIHGGKAVIKSPADAVAHGIGYLSEDRKHFGLAVGMDVQANIAL 374
           +   + G     A  + + G       P      GI    E+R     A  M +  N  L
Sbjct: 296 LLGVLSGETTTAADAVTLDGAPIGNLGPVARRRLGILAAPEERLGHAAAPDMSLTENAML 355

Query: 375 SSMGR--FTRVGFMDQRAIREAAQMYVRQLAIKTPSVEQQARLLSGGNQQKIVIAKWLLR 432
           ++  R      GF+     +E A+  ++   ++TP  E  AR LSGGN QK VI + +L+
Sbjct: 356 TAATREGLASRGFLKWGLAQEFAEKVIKSFDVRTPGPENAARSLSGGNLQKFVIGREVLQ 415

Query: 433 DCDILFFDEPTRGIDVGAKSEIYKLLDALAEQGKAIVMISSELPEVLRMSHRVLVMCEGR 492
             D+L  ++PT G+D  A + I + L  LA  G A++ IS +L E++ ++     + EGR
Sbjct: 416 RPDVLVVNQPTWGVDAAAAAAIRQSLLDLAAGGTAVICISQDLDELMEIADSFAALNEGR 475

Query: 493 ITGELARADATQEKI 507
           ++     A  + ++I
Sbjct: 476 LSAPRPTAGLSVDEI 490



 Score = 77.4 bits (189), Expect = 1e-18
 Identities = 63/239 (26%), Positives = 113/239 (47%), Gaps = 16/239 (6%)

Query: 277 VLEVRGLNR---GRAIRD-VSFTLRKGEILGFAGLMGAGRTEVARAIFGADPLEAGEIII 332
           +L ++GL +   G    D VSF +  GE+    G  GAG++ + + I+G    ++G++++
Sbjct: 5   LLSLQGLTKAYPGVVANDTVSFDIGAGEVHALLGENGAGKSTLVKMIYGLVKPDSGKMLL 64

Query: 333 HGGKAVIKSPADAVAHGIGYLSEDRKHFGLAVGMDVQANIALSSMGRFTRVGFMDQRA-I 391
           HG       P  A A GI  + +   HF L   ++V  NIAL   G  T     D    I
Sbjct: 65  HGEPYTPGEPRQARADGIAMVFQ---HFSLFDALNVAENIAL---GMETPPALRDLATQI 118

Query: 392 REAAQMYVRQLAIKTPSVEQQARLLSGGNQQKIVIAKWLLRDCDILFFDEPTRGIDVGAK 451
           R+ ++ Y   L        +    LS G +Q++ I + LL+D  +L  DEPT  +     
Sbjct: 119 RKVSETYGLPL-----DPYRTVGDLSAGERQRVEIIRCLLQDPKLLIMDEPTSVLTPQEV 173

Query: 452 SEIYKLLDALAEQGKAIVMISSELPEVLRMSHRVLVMCEGRITGELARADATQEKIMQL 510
             +++ L  L  +G +I+ IS +L E+  +     ++  G+  GE   ++ +   + ++
Sbjct: 174 EILFQTLQKLRSEGTSILYISHKLEEIRTLCDHATILRLGKNVGECVPSETSARDMAEM 232



 Score = 67.0 bits (162), Expect = 2e-15
 Identities = 63/233 (27%), Positives = 102/233 (43%), Gaps = 16/233 (6%)

Query: 37  ALDNCQFELAAGEVHALMGENGAGKSTLMKILSGVYQRDSGDILLDGKPVEITEPRQAQA 96
           AL N    +  GE+  + G  G G+  L+ +LSG     +  + LDG P+    P   + 
Sbjct: 269 ALKNVHMTVRKGEILGVGGVAGNGQDELLGVLSGETTTAADAVTLDGAPIGNLGPVARRR 328

Query: 97  LGIGIIHQELNLMNH-----LSAAQNIFIGREPRKAMGLFIDEDELNRQAAAIFARMRL- 150
           LGI    +E   + H     +S  +N  +    R+ +        L    A  FA   + 
Sbjct: 329 LGILAAPEER--LGHAAAPDMSLTENAMLTAATREGLA---SRGFLKWGLAQEFAEKVIK 383

Query: 151 DMDPSTPVGE-----LTVARQQMVEIAKALSFDSRVLIMDEPTAALNNAEIAELFRIIRD 205
             D  TP  E     L+    Q   I + +     VL++++PT  ++ A  A + + + D
Sbjct: 384 SFDVRTPGPENAARSLSGGNLQKFVIGREVLQRPDVLVVNQPTWGVDAAAAAAIRQSLLD 443

Query: 206 LQAQGVGIVYISHKMDELRQIADRVSVMRDGKYIATVPMQETSMDTIISMMVG 258
           L A G  ++ IS  +DEL +IAD  + + +G+  A  P    S+D I  MM G
Sbjct: 444 LAAGGTAVICISQDLDELMEIADSFAALNEGRLSAPRPTAGLSVDEIGLMMGG 496


Lambda     K      H
   0.320    0.135    0.372 

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: 589
Number of extensions: 35
Number of successful extensions: 8
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 3
Length of query: 520
Length of database: 505
Length adjustment: 35
Effective length of query: 485
Effective length of database: 470
Effective search space:   227950
Effective search space used:   227950
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