Alignments for a candidate for HSERO_RS05250 in Streptacidiphilus oryzae TH49

GapMind for catabolism of small carbon sources

Alignments for a candidate for HSERO_RS05250 in Streptacidiphilus oryzae TH49

Align Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale)
to candidate WP_084703690.1 BS73_RS01755 sugar ABC transporter ATP-binding protein

Query= uniprot:D8J111
         (520 letters)



>NCBI__GCF_000744815.1:WP_084703690.1
          Length = 533

 Score =  451 bits (1161), Expect = e-131
 Identities = 240/496 (48%), Positives = 332/496 (66%), Gaps = 6/496 (1%)

Query: 17  SSSVPVIALRNVCKRFPGVLALDNCQFELAAGEVHALMGENGAGKSTLMKILSGVYQRDS 76
           + S  ++ L  V K FPGV+ALD   F+L  GEVH L+GENGAGKSTL+K+LSG ++ D 
Sbjct: 18  AGSAELLRLEGVRKTFPGVVALDRVDFDLRRGEVHVLLGENGAGKSTLIKVLSGAHRPDR 77

Query: 77  GDILLDGKPVEITEPRQAQALGIGIIHQELNLMNHLSAAQNIFIGREPRKAMGLFIDEDE 136
           G +L+DG  V I   + A+ LGI  I+QE NL+  LS A+NIF+GR+PR+    F+D   
Sbjct: 78  GRVLVDGAEVRINGAQDAERLGIATIYQEFNLVPELSVAENIFLGRQPRRYG--FVDRRR 135

Query: 137 LNRQAAAIFARMRLDMDPSTPVGELTVARQQMVEIAKALSFDSRVLIMDEPTAALNNAEI 196
           +  +AA +  R+ LD+ P T V EL +A +QMVEIAKALS  +RVLIMDEPTA L   E+
Sbjct: 136 MQEEAAELLKRVGLDVPPRTRVAELGIAGRQMVEIAKALSLRARVLIMDEPTAVLTTEEV 195

Query: 197 AELFRIIRDLQAQGVGIVYISHKMDELRQIADRVSVMRDGKYIATVPMQETSMDTIISMM 256
            +LF I+R L+A GVG+V+I+H ++E+  + DRV+V+RDG+ +  VP  +T  D ++ +M
Sbjct: 196 EKLFAIVRALRADGVGVVFITHHLEEIAALGDRVTVLRDGRSVDQVPA-DTDQDELVRLM 254

Query: 257 VGRALDGEQ-RIPPDTSRNDVVLEVRGLNRGRAIRDVSFTLRKGEILGFAGLMGAGRTEV 315
           VGR ++ +  R  P+    + +L VRGL      RDV F +R GE++G AGL+GAGRTEV
Sbjct: 255 VGREIEAQYPRERPELG--EPLLRVRGLTSAGVFRDVDFEVRAGEVVGLAGLVGAGRTEV 312

Query: 316 ARAIFGADPLEAGEIIIHGGKAVIKSPADAVAHGIGYLSEDRKHFGLAVGMDVQANIALS 375
            RA+FGADP ++G + + G          A+A GIG + EDRK  GL +   ++ N+ L 
Sbjct: 313 VRAVFGADPYDSGSVEVEGRPVRPGDVNAAMAAGIGLVPEDRKAQGLVLDAPIEENLGLV 372

Query: 376 SMGRFTRVGFMDQRAIREAAQMYVRQLAIKTPSVEQQARLLSGGNQQKIVIAKWLLRDCD 435
           ++GR  R GF+D+   R +A     +L ++   ++Q A  LSGGNQQK+VI KWLL    
Sbjct: 373 TLGRTARYGFVDRSGQRASAAGIAERLRVRMAGLDQPAGTLSGGNQQKLVIGKWLLAGSR 432

Query: 436 ILFFDEPTRGIDVGAKSEIYKLLDALAEQGKAIVMISSELPEVLRMSHRVLVMCEGRITG 495
           +L  DEPTRGIDVGAK EIY+L++ L   G A++M+SS+LPEVL MS RVLVM +GRI G
Sbjct: 433 VLILDEPTRGIDVGAKVEIYQLVNELTASGHAVLMVSSDLPEVLGMSDRVLVMAQGRIAG 492

Query: 496 ELARADATQEKIMQLA 511
           EL  A A+Q+ +M LA
Sbjct: 493 ELDPARASQDDVMALA 508



 Score =  105 bits (262), Expect = 4e-27
 Identities = 67/219 (30%), Positives = 114/219 (52%), Gaps = 4/219 (1%)

Query: 43  FELAAGEVHALMGENGAGKSTLMKILSGVYQRDSGDILLDGKPVEITEPRQAQALGIGII 102
           FE+ AGEV  L G  GAG++ +++ + G    DSG + ++G+PV   +   A A GIG++
Sbjct: 291 FEVRAGEVVGLAGLVGAGRTEVVRAVFGADPYDSGSVEVEGRPVRPGDVNAAMAAGIGLV 350

Query: 103 HQELNLMNHLSAA---QNIFIGREPRKAMGLFIDEDELNRQAAAIFARMRLDMDP-STPV 158
            ++      +  A   +N+ +    R A   F+D       AA I  R+R+ M     P 
Sbjct: 351 PEDRKAQGLVLDAPIEENLGLVTLGRTARYGFVDRSGQRASAAGIAERLRVRMAGLDQPA 410

Query: 159 GELTVARQQMVEIAKALSFDSRVLIMDEPTAALNNAEIAELFRIIRDLQAQGVGIVYISH 218
           G L+   QQ + I K L   SRVLI+DEPT  ++     E+++++ +L A G  ++ +S 
Sbjct: 411 GTLSGGNQQKLVIGKWLLAGSRVLILDEPTRGIDVGAKVEIYQLVNELTASGHAVLMVSS 470

Query: 219 KMDELRQIADRVSVMRDGKYIATVPMQETSMDTIISMMV 257
            + E+  ++DRV VM  G+    +     S D ++++ V
Sbjct: 471 DLPEVLGMSDRVLVMAQGRIAGELDPARASQDDVMALAV 509


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: 745
Number of extensions: 44
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: 520
Length of database: 533
Length adjustment: 35
Effective length of query: 485
Effective length of database: 498
Effective search space:   241530
Effective search space used:   241530
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 24 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 2024 update 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