GapMind for catabolism of small carbon sources

 

Alignments for a candidate for HSERO_RS03640 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:D8IZC7
         (521 letters)



>NCBI__GCF_001623255.1:WP_068005521.1
          Length = 515

 Score =  276 bits (705), Expect = 2e-78
 Identities = 166/505 (32%), Positives = 292/505 (57%), Gaps = 23/505 (4%)

Query: 2   TQTPLLQMRGIRKSFGATLALSDMHLTIRPGEIHALMGENGAGKSTLMKVLSGVHAPDQG 61
           T  PLL ++ I K FG  +A  +++L +  GEI AL+GENGAGK+TLM +L G +  D+G
Sbjct: 6   TVHPLLSLQNITKIFGDLVANGNVNLDLHAGEIVALLGENGAGKTTLMNILFGHYVADEG 65

Query: 62  EILLDGRPVALRD--PGASRAA---GINLIYQELAVAPNISVAANVFMGSELRTRLGLID 116
            +++      L D  PGA +AA   GI +++Q   +A N++   N+ +G+E      L  
Sbjct: 66  RVMVRTSSGTLVDLEPGAPQAALEAGIGMVHQHFTLAENLTGLENIVLGTE-----SLFA 120

Query: 117 HAAMRSRTDAVLRQLGAGFGAS---DL-AGRLSIAEQQQVEIARALVHRSRIVIMDEPTA 172
               RS+  A L++L    G     DL   +L++ E+Q+VEI +AL   +RI+++DEPTA
Sbjct: 121 RKFSRSKARAKLQELMQSSGLEVDLDLRVSKLAVGERQRVEILKALYRDARILVLDEPTA 180

Query: 173 ALSERETEQLFNVVRRLRDEGLAIIYISHRMAEVYALADRVTVLRDGSFVGELVRDEIDS 232
            L+ +E++ LFN ++ L  +G+AII+ISH+MAEV   +DRV VLR G  V +L   + D 
Sbjct: 181 VLTPQESDSLFNTLKLLAAKGMAIIFISHKMAEVLGASDRVAVLRGGRIVADLPTSQCDR 240

Query: 233 ERIVQMMVGRSLSEFYQHQRIAPADAAQLPTVMQVRALAGGK--IRPASFDVRAGEVLGF 290
            ++ ++MVG ++    Q     P +  +   V +  +   G+  I   +  +R GE++G 
Sbjct: 241 HKLAELMVGHAV----QMAEREPGNPGEEILVFKGVSAGEGRELIENVNLSLRKGEIIGL 296

Query: 291 AGLVGAGRTELARLLFGADPRSGGDILLEGRPVHIDQPRAAMRAGIAYVPEDRKGQGLFL 350
           AG+ G G++ LA++L G +  + G + L  +P+  +   AA+++G+A +PEDR   G+  
Sbjct: 297 AGVSGNGQSMLAKVLSGLEEPTAGAVTLGSQPLKAN-AAAAIQSGVARIPEDRHHDGIVG 355

Query: 351 QMAVAANATMNVASR--HTRLGLVRSRSLGGVARAAIQRLNVKVAHPETPVGKLSGGNQQ 408
            M+V  N  +    +  + R GL+R   +   A+ AI+  +++ + P      LSGGN Q
Sbjct: 356 AMSVEENLVLEEIRKPAYQRFGLLRFNEIRKRAQEAIKAYDIRCSGPLAVSRLLSGGNIQ 415

Query: 409 KVLLARWLEIAPKVLILDEPTRGVDIYAKSEIYQLVHRLASQGVAVVVISSELPEVIGIC 468
           K++LAR L+  P +++  +P+RG+D+ A +++++ +     +G  V++IS +L E+  + 
Sbjct: 416 KIVLARTLDQEPAIVLAAQPSRGLDVGATADVHRRLQEARDRGAGVLLISEDLDELFQLS 475

Query: 469 DRVLVMREGMITGELAGAAITQENI 493
           DR+ V+  G ++  +A   + ++ +
Sbjct: 476 DRIAVIHRGHVSEPMASEELDKKQV 500



 Score = 88.2 bits (217), Expect = 7e-22
 Identities = 66/246 (26%), Positives = 119/246 (48%), Gaps = 11/246 (4%)

Query: 6   LLQMRGIRKSFGATLALSDMHLTIRPGEIHALMGENGAGKSTLMKVLSGVHAPDQGEILL 65
           +L  +G+    G  L + +++L++R GEI  L G +G G+S L KVLSG+  P  G + L
Sbjct: 266 ILVFKGVSAGEGREL-IENVNLSLRKGEIIGLAGVSGNGQSMLAKVLSGLEEPTAGAVTL 324

Query: 66  DGRPVALRDPGASRAAGINLIYQEL---AVAPNISVAANVFMGSELRT----RLGLIDHA 118
             +P+   +  A+  +G+  I ++     +   +SV  N+ +  E+R     R GL+   
Sbjct: 325 GSQPLKA-NAAAAIQSGVARIPEDRHHDGIVGAMSVEENLVL-EEIRKPAYQRFGLLRFN 382

Query: 119 AMRSRTDAVLRQLGAGFGASDLAGRL-SIAEQQQVEIARALVHRSRIVIMDEPTAALSER 177
            +R R    ++             RL S    Q++ +AR L     IV+  +P+  L   
Sbjct: 383 EIRKRAQEAIKAYDIRCSGPLAVSRLLSGGNIQKIVLARTLDQEPAIVLAAQPSRGLDVG 442

Query: 178 ETEQLFNVVRRLRDEGLAIIYISHRMAEVYALADRVTVLRDGSFVGELVRDEIDSERIVQ 237
            T  +   ++  RD G  ++ IS  + E++ L+DR+ V+  G     +  +E+D +++  
Sbjct: 443 ATADVHRRLQEARDRGAGVLLISEDLDELFQLSDRIAVIHRGHVSEPMASEELDKKQVGL 502

Query: 238 MMVGRS 243
           MM G S
Sbjct: 503 MMAGHS 508



 Score = 79.3 bits (194), Expect = 3e-19
 Identities = 65/226 (28%), Positives = 109/226 (48%), Gaps = 17/226 (7%)

Query: 279 SFDVRAGEVLGFAGLVGAGRTELARLLFGADPRSGGDILLE---GRPVHIDQ--PRAAMR 333
           + D+ AGE++   G  GAG+T L  +LFG      G +++    G  V ++   P+AA+ 
Sbjct: 30  NLDLHAGEIVALLGENGAGKTTLMNILFGHYVADEGRVMVRTSSGTLVDLEPGAPQAALE 89

Query: 334 AGIAYVPEDRKGQGLFLQMAVAANATMNVASRHTRLGLVRSRSLGGVARAAIQRLNVKVA 393
           AGI  V +      L   +    N  +   S   R    RS+     ARA +Q L     
Sbjct: 90  AGIGMVHQHFT---LAENLTGLENIVLGTESLFARK-FSRSK-----ARAKLQELMQSSG 140

Query: 394 HP---ETPVGKLSGGNQQKVLLARWLEIAPKVLILDEPTRGVDIYAKSEIYQLVHRLASQ 450
                +  V KL+ G +Q+V + + L    ++L+LDEPT  +       ++  +  LA++
Sbjct: 141 LEVDLDLRVSKLAVGERQRVEILKALYRDARILVLDEPTAVLTPQESDSLFNTLKLLAAK 200

Query: 451 GVAVVVISSELPEVIGICDRVLVMREGMITGELAGAAITQENIMRL 496
           G+A++ IS ++ EV+G  DRV V+R G I  +L  +   +  +  L
Sbjct: 201 GMAIIFISHKMAEVLGASDRVAVLRGGRIVADLPTSQCDRHKLAEL 246


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: 634
Number of extensions: 35
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: 521
Length of database: 515
Length adjustment: 35
Effective length of query: 486
Effective length of database: 480
Effective search space:   233280
Effective search space used:   233280
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