Alignments for a candidate for HSERO_RS03640 in Phaeobacter inhibens BS107

GapMind for catabolism of small carbon sources

Alignments for a candidate for HSERO_RS03640 in Phaeobacter inhibens BS107

Align Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale)
to candidate GFF385 PGA1_c03960 ribose import ATP-binding protein RbsA

Query= uniprot:D8IZC7
         (521 letters)



>FitnessBrowser__Phaeo:GFF385
          Length = 509

 Score =  277 bits (708), Expect = 8e-79
 Identities = 169/490 (34%), Positives = 272/490 (55%), Gaps = 19/490 (3%)

Query: 5   PLLQMRGIRKSFGATLALSDMHLTIRPGEIHALMGENGAGKSTLMKVLSGVHAPDQGEIL 64
           P ++++GI K+FG   A  D+ + + PG IH ++GENGAGKSTLM +L G +  D+GE+ 
Sbjct: 4   PAIELKGISKAFGPVQANKDISIRVAPGTIHGIIGENGAGKSTLMSILYGFYKADKGEVW 63

Query: 65  LDGRPVALRDPGASRAAGINLIYQELAVAPNISVAANVFMGSELRTRLGLIDHAAMRSRT 124
           + G+   + D  A+ +AGI +++Q   +  N +V  N+ +G+E     GL+  +  ++R 
Sbjct: 64  IHGKRTEIPDSQAAISAGIGMVFQHFKLVENFTVLENIILGAE---DGGLLKPSLSKARK 120

Query: 125 DAVLRQLGAGFGAS-DLAGR---LSIAEQQQVEIARALVHRSRIVIMDEPTAALSERETE 180
              L+ L A +  + D   R   + +  QQ+VEI +AL  ++ I+I+DEPT  L+  E +
Sbjct: 121 S--LKDLAAEYELNVDPDARIDEIGVGMQQRVEILKALYRQADILILDEPTGVLTPAEAD 178

Query: 181 QLFNVVRRLRDEGLAIIYISHRMAEVYALADRVTVLRDGSFVGELVRDEIDSERIVQMMV 240
           QLF ++ RLR EG  II I+H++ E+    D V+V+R G     +   E   E + ++MV
Sbjct: 179 QLFRILDRLRAEGKTIILITHKLREIMEYTDTVSVMRRGEMTATVKTAETSPEHLAELMV 238

Query: 241 GRSLSEFYQHQRIAPA-DAAQLPTVMQVRALAGGKIRPASFDVRAGEVLGFAGLVGAGRT 299
           GR +          P     ++  +  V      +++     VRAGE+LG AG+ G G++
Sbjct: 239 GRKVLLRVDKVPATPGKPILEIENLSVVDEAGVARVKNIDLTVRAGEILGIAGVAGNGQS 298

Query: 300 ELARLLFGADPRSG-GDILLEGRPVHI----DQPRAAMRAGIAYVPEDRKGQGLFLQMAV 354
           EL  +L G   R G G I L G P+ +       RA   A +A+VPEDR+ +GL +    
Sbjct: 299 ELMEVLGGM--REGQGSIRLNGAPLPLSGAGSDARARRAAHVAHVPEDRQREGLIMDFHA 356

Query: 355 AANATMNV--ASRHTRLGLVRSRSLGGVARAAIQRLNVKVAHPETPVGKLSGGNQQKVLL 412
             N       A  + R  L+ + +L     A + + +V+   P       SGGNQQK+++
Sbjct: 357 WENVAFGYHHAPEYQRGLLMNNAALRADTEAKMAKFDVRPPDPWLAAKNFSGGNQQKIVV 416

Query: 413 ARWLEIAPKVLILDEPTRGVDIYAKSEIYQLVHRLASQGVAVVVISSELPEVIGICDRVL 472
           AR +E  P++L++ +PTRGVDI A   I++ +  L  QG A++++S EL E++ + DRV 
Sbjct: 417 AREIERNPELLLIGQPTRGVDIGAIEFIHKQIVELRDQGKAILLVSVELEEILSLADRVA 476

Query: 473 VMREGMITGE 482
           VM +GMI GE
Sbjct: 477 VMFDGMIMGE 486



 Score = 93.2 bits (230), Expect = 2e-23
 Identities = 75/250 (30%), Positives = 128/250 (51%), Gaps = 15/250 (6%)

Query: 5   PLLQMRGIRKSFGATLA-LSDMHLTIRPGEIHALMGENGAGKSTLMKVLSGVHAPDQGEI 63
           P+L++  +     A +A + ++ LT+R GEI  + G  G G+S LM+VL G+    QG I
Sbjct: 256 PILEIENLSVVDEAGVARVKNIDLTVRAGEILGIAGVAGNGQSELMEVLGGMRE-GQGSI 314

Query: 64  LLDGRPVALRDPG----ASRAAGINLI---YQELAVAPNISVAANVFMG----SELRTRL 112
            L+G P+ L   G    A RAA +  +    Q   +  +     NV  G     E +  L
Sbjct: 315 RLNGAPLPLSGAGSDARARRAAHVAHVPEDRQREGLIMDFHAWENVAFGYHHAPEYQRGL 374

Query: 113 GLIDHAAMRSRTDAVLRQLGAGFGASDLAGR-LSIAEQQQVEIARALVHRSRIVIMDEPT 171
            L+++AA+R+ T+A + +         LA +  S   QQ++ +AR +     ++++ +PT
Sbjct: 375 -LMNNAALRADTEAKMAKFDVRPPDPWLAAKNFSGGNQQKIVVAREIERNPELLLIGQPT 433

Query: 172 AALSERETEQLFNVVRRLRDEGLAIIYISHRMAEVYALADRVTVLRDGSFVGELVRDEID 231
             +     E +   +  LRD+G AI+ +S  + E+ +LADRV V+ DG  +GE   D+ D
Sbjct: 434 RGVDIGAIEFIHKQIVELRDQGKAILLVSVELEEILSLADRVAVMFDGMIMGERPADQTD 493

Query: 232 SERIVQMMVG 241
            + +  +M G
Sbjct: 494 EKELGLLMAG 503



 Score = 77.0 bits (188), Expect = 1e-18
 Identities = 63/229 (27%), Positives = 108/229 (47%), Gaps = 16/229 (6%)

Query: 279 SFDVRAGEVLGFAGLVGAGRTELARLLFGADPRSGGDILLEGRPVHIDQPRAAMRAGIAY 338
           S  V  G + G  G  GAG++ L  +L+G      G++ + G+   I   +AA+ AGI  
Sbjct: 25  SIRVAPGTIHGIIGENGAGKSTLMSILYGFYKADKGEVWIHGKRTEIPDSQAAISAGIGM 84

Query: 339 VPEDRKGQGLFLQMAVAANATMNVASRHTRLGLVRSRSLGGVAR-----AAIQRLNVKVA 393
           V +  K   L     V  N  +         GL++  SL    +     AA   LNV   
Sbjct: 85  VFQHFK---LVENFTVLENIILGAEDG----GLLKP-SLSKARKSLKDLAAEYELNVD-- 134

Query: 394 HPETPVGKLSGGNQQKVLLARWLEIAPKVLILDEPTRGVDIYAKSEIYQLVHRLASQGVA 453
            P+  + ++  G QQ+V + + L     +LILDEPT  +      ++++++ RL ++G  
Sbjct: 135 -PDARIDEIGVGMQQRVEILKALYRQADILILDEPTGVLTPAEADQLFRILDRLRAEGKT 193

Query: 454 VVVISSELPEVIGICDRVLVMREGMITGELAGAAITQENIMRLATDTNV 502
           +++I+ +L E++   D V VMR G +T  +  A  + E++  L     V
Sbjct: 194 IILITHKLREIMEYTDTVSVMRRGEMTATVKTAETSPEHLAELMVGRKV 242


Lambda     K      H
   0.320    0.135    0.378 

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: 677
Number of extensions: 33
Number of successful extensions: 9
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: 521
Length of database: 509
Length adjustment: 35
Effective length of query: 486
Effective length of database: 474
Effective search space:   230364
Effective search space used:   230364
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