GapMind for catabolism of small carbon sources

 

Alignments for a candidate for HSERO_RS05250 in Pseudovibrio axinellae Ad2

Align Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale)
to candidate WP_068005521.1 PsAD2_RS10155 ABC transporter ATP-binding protein

Query= uniprot:D8J111
         (520 letters)



>NCBI__GCF_001623255.1:WP_068005521.1
          Length = 515

 Score =  283 bits (724), Expect = 1e-80
 Identities = 168/498 (33%), Positives = 288/498 (57%), Gaps = 17/498 (3%)

Query: 21  PVIALRNVCKRFPGVLALDNCQFELAAGEVHALMGENGAGKSTLMKILSGVYQRDSGDIL 80
           P+++L+N+ K F  ++A  N   +L AGE+ AL+GENGAGK+TLM IL G Y  D G ++
Sbjct: 9   PLLSLQNITKIFGDLVANGNVNLDLHAGEIVALLGENGAGKTTLMNILFGHYVADEGRVM 68

Query: 81  L---DGKPVEITE--PRQAQALGIGIIHQELNLMNHLSAAQNIFIGREPRKAMGLFIDED 135
           +    G  V++    P+ A   GIG++HQ   L  +L+  +NI +G E      LF  + 
Sbjct: 69  VRTSSGTLVDLEPGAPQAALEAGIGMVHQHFTLAENLTGLENIVLGTE-----SLFARKF 123

Query: 136 ELNRQAAAIFARMR---LDMDPSTPVGELTVARQQMVEIAKALSFDSRVLIMDEPTAALN 192
             ++  A +   M+   L++D    V +L V  +Q VEI KAL  D+R+L++DEPTA L 
Sbjct: 124 SRSKARAKLQELMQSSGLEVDLDLRVSKLAVGERQRVEILKALYRDARILVLDEPTAVLT 183

Query: 193 NAEIAELFRIIRDLQAQGVGIVYISHKMDELRQIADRVSVMRDGKYIATVPMQETSMDTI 252
             E   LF  ++ L A+G+ I++ISHKM E+   +DRV+V+R G+ +A +P  +     +
Sbjct: 184 PQESDSLFNTLKLLAAKGMAIIFISHKMAEVLGASDRVAVLRGGRIVADLPTSQCDRHKL 243

Query: 253 ISMMVGRALDGEQRIPPDTSRNDVVLEVRGLNRGR-AIRDVSFTLRKGEILGFAGLMGAG 311
             +MVG A+   +R P +     +V +      GR  I +V+ +LRKGEI+G AG+ G G
Sbjct: 244 AELMVGHAVQMAEREPGNPGEEILVFKGVSAGEGRELIENVNLSLRKGEIIGLAGVSGNG 303

Query: 312 RTEVARAIFGADPLEAGEIIIHGGKAVIKSPADAVAHGIGYLSEDRKHFGLAVGMDVQAN 371
           ++ +A+ + G +   AG + + G + +  + A A+  G+  + EDR H G+   M V+ N
Sbjct: 304 QSMLAKVLSGLEEPTAGAVTL-GSQPLKANAAAAIQSGVARIPEDRHHDGIVGAMSVEEN 362

Query: 372 IALSSMGR--FTRVGFMDQRAIREAAQMYVRQLAIKTPSVEQQARLLSGGNQQKIVIAKW 429
           + L  + +  + R G +    IR+ AQ  ++   I+       +RLLSGGN QKIV+A+ 
Sbjct: 363 LVLEEIRKPAYQRFGLLRFNEIRKRAQEAIKAYDIRCSGPLAVSRLLSGGNIQKIVLART 422

Query: 430 LLRDCDILFFDEPTRGIDVGAKSEIYKLLDALAEQGKAIVMISSELPEVLRMSHRVLVMC 489
           L ++  I+   +P+RG+DVGA +++++ L    ++G  +++IS +L E+ ++S R+ V+ 
Sbjct: 423 LDQEPAIVLAAQPSRGLDVGATADVHRRLQEARDRGAGVLLISEDLDELFQLSDRIAVIH 482

Query: 490 EGRITGELARADATQEKI 507
            G ++  +A  +  ++++
Sbjct: 483 RGHVSEPMASEELDKKQV 500



 Score = 88.6 bits (218), Expect = 5e-22
 Identities = 64/225 (28%), Positives = 106/225 (47%), Gaps = 11/225 (4%)

Query: 291 DVSFTLRKGEILGFAGLMGAGRTEVARAIFGADPLEAGEIIIHGGKAVIK-----SPADA 345
           +V+  L  GEI+   G  GAG+T +   +FG    + G +++      +      +P  A
Sbjct: 28  NVNLDLHAGEIVALLGENGAGKTTLMNILFGHYVADEGRVMVRTSSGTLVDLEPGAPQAA 87

Query: 346 VAHGIGYLSEDRKHFGLAVGMDVQANIALSSMGRFTRVGFMDQRAIREAAQMYVRQLAIK 405
           +  GIG + +   HF LA  +    NI L +   F R     +   R   Q  ++   ++
Sbjct: 88  LEAGIGMVHQ---HFTLAENLTGLENIVLGTESLFARK--FSRSKARAKLQELMQSSGLE 142

Query: 406 TPSVEQQARLLSGGNQQKIVIAKWLLRDCDILFFDEPTRGIDVGAKSEIYKLLDALAEQG 465
              ++ +   L+ G +Q++ I K L RD  IL  DEPT  +       ++  L  LA +G
Sbjct: 143 V-DLDLRVSKLAVGERQRVEILKALYRDARILVLDEPTAVLTPQESDSLFNTLKLLAAKG 201

Query: 466 KAIVMISSELPEVLRMSHRVLVMCEGRITGELARADATQEKIMQL 510
            AI+ IS ++ EVL  S RV V+  GRI  +L  +   + K+ +L
Sbjct: 202 MAIIFISHKMAEVLGASDRVAVLRGGRIVADLPTSQCDRHKLAEL 246



 Score = 80.1 bits (196), Expect = 2e-19
 Identities = 58/234 (24%), Positives = 115/234 (49%), Gaps = 7/234 (2%)

Query: 38  LDNCQFELAAGEVHALMGENGAGKSTLMKILSGVYQRDSGDILLDGKPVEITEPRQAQAL 97
           ++N    L  GE+  L G +G G+S L K+LSG+ +  +G + L  +P++       Q+ 
Sbjct: 281 IENVNLSLRKGEIIGLAGVSGNGQSMLAKVLSGLEEPTAGAVTLGSQPLKANAAAAIQS- 339

Query: 98  GIGIIHQELN---LMNHLSAAQNIFIG--REPR-KAMGLFIDEDELNRQAAAIFARMRLD 151
           G+  I ++ +   ++  +S  +N+ +   R+P  +  GL    +   R   AI A     
Sbjct: 340 GVARIPEDRHHDGIVGAMSVEENLVLEEIRKPAYQRFGLLRFNEIRKRAQEAIKAYDIRC 399

Query: 152 MDPSTPVGELTVARQQMVEIAKALSFDSRVLIMDEPTAALNNAEIAELFRIIRDLQAQGV 211
             P      L+    Q + +A+ L  +  +++  +P+  L+    A++ R +++ + +G 
Sbjct: 400 SGPLAVSRLLSGGNIQKIVLARTLDQEPAIVLAAQPSRGLDVGATADVHRRLQEARDRGA 459

Query: 212 GIVYISHKMDELRQIADRVSVMRDGKYIATVPMQETSMDTIISMMVGRALDGEQ 265
           G++ IS  +DEL Q++DR++V+  G     +  +E     +  MM G +  GEQ
Sbjct: 460 GVLLISEDLDELFQLSDRIAVIHRGHVSEPMASEELDKKQVGLMMAGHSAKGEQ 513


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: 545
Number of extensions: 33
Number of successful extensions: 10
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: 515
Length adjustment: 35
Effective length of query: 485
Effective length of database: 480
Effective search space:   232800
Effective search space used:   232800
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:

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