GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PS417_12065 in Pseudovibrio axinellae Ad2

Align D-ribose transporter ATP-binding protein; SubName: Full=Putative xylitol transport system ATP-binding protein; SubName: Full=Sugar ABC transporter ATP-binding protein (characterized, see rationale)
to candidate WP_068005521.1 PsAD2_RS10155 ABC transporter ATP-binding protein

Query= uniprot:A0A1N7TX47
         (495 letters)



>NCBI__GCF_001623255.1:WP_068005521.1
          Length = 515

 Score =  229 bits (583), Expect = 2e-64
 Identities = 148/482 (30%), Positives = 251/482 (52%), Gaps = 16/482 (3%)

Query: 6   LLQAEHVAKAYAGVPALRDGRLSLRAGSVHALCGGNGAGKSTFLSILMGITQRDAGSILL 65
           LL  +++ K +  + A  +  L L AG + AL G NGAGK+T ++IL G    D G +++
Sbjct: 10  LLSLQNITKIFGDLVANGNVNLDLHAGEIVALLGENGAGKTTLMNILFGHYVADEGRVMV 69

Query: 66  NGAP-----VQFNRPSEALAAGIAMITQELEPIPYMTVAENIWLGREPRRAGCIVDNKAL 120
             +      ++   P  AL AGI M+ Q       +T  ENI LG E   A     +KA 
Sbjct: 70  RTSSGTLVDLEPGAPQAALEAGIGMVHQHFTLAENLTGLENIVLGTESLFARKFSRSKA- 128

Query: 121 NRRTRELLDSLEFDVDATSPMHRLSVAQIQLVEIAKAFSHDCQVMIMDEPTSAIGEHEAQ 180
             + +EL+ S   +VD    + +L+V + Q VEI KA   D +++++DEPT+ +   E+ 
Sbjct: 129 RAKLQELMQSSGLEVDLDLRVSKLAVGERQRVEILKALYRDARILVLDEPTAVLTPQESD 188

Query: 181 TLFKAIRRLTAQGAGIVYVSHRLSELAQIADDYSIFRDGAFVESGRMADIDRDHLVRGIV 240
           +LF  ++ L A+G  I+++SH+++E+   +D  ++ R G  V     +  DR  L   +V
Sbjct: 189 SLFNTLKLLAAKGMAIIFISHKMAEVLGASDRVAVLRGGRIVADLPTSQCDRHKLAELMV 248

Query: 241 GQELTRIDHKVGRECAANTCLQVDNLSRAGE----FHDISLQLRQGEILGIYGLMGSGRS 296
           G  +   + + G        L    +S AGE      +++L LR+GEI+G+ G+ G+G+S
Sbjct: 249 GHAVQMAEREPGN--PGEEILVFKGVS-AGEGRELIENVNLSLRKGEIIGLAGVSGNGQS 305

Query: 297 EFLNCIYGLTVADSGSVTLQGKPMPIGLPKATINAGMSLVTEDRKDSGLVLTGSILSNIA 356
                + GL    +G+VTL  +P+      A I +G++ + EDR   G+V   S+  N+ 
Sbjct: 306 MLAKVLSGLEEPTAGAVTLGSQPLKAN-AAAAIQSGVARIPEDRHHDGIVGAMSVEENLV 364

Query: 357 LSAYKR--LSSWSLINARKETQLAEDMVKRLQIKTTSLELPVASMSGGNQQKVVLAKCLS 414
           L   ++     + L+   +  + A++ +K   I+ +        +SGGN QK+VLA+ L 
Sbjct: 365 LEEIRKPAYQRFGLLRFNEIRKRAQEAIKAYDIRCSGPLAVSRLLSGGNIQKIVLARTLD 424

Query: 415 TEPVCLLCDEPTRGIDEGAKQEIYHLLDQFVRGGGAAIVVSSEAPELLHLSDRIAVFKGG 474
            EP  +L  +P+RG+D GA  +++  L +    G   +++S +  EL  LSDRIAV   G
Sbjct: 425 QEPAIVLAAQPSRGLDVGATADVHRRLQEARDRGAGVLLISEDLDELFQLSDRIAVIHRG 484

Query: 475 RL 476
            +
Sbjct: 485 HV 486



 Score = 82.0 bits (201), Expect = 4e-20
 Identities = 62/212 (29%), Positives = 106/212 (50%), Gaps = 17/212 (8%)

Query: 274 DISLQLRQGEILGIYGLMGSGRSEFLNCIYGLTVADSGSVTLQGKPMPI-----GLPKAT 328
           +++L L  GEI+ + G  G+G++  +N ++G  VAD G V ++     +     G P+A 
Sbjct: 28  NVNLDLHAGEIVALLGENGAGKTTLMNILFGHYVADEGRVMVRTSSGTLVDLEPGAPQAA 87

Query: 329 INAGMSLVTEDRKDSGLVLTGSILSNIAL---SAYKRLSSWSLINARKETQLAEDMVKRL 385
           + AG+ +V +        LTG  L NI L   S + R  S S   A+ +  +    ++  
Sbjct: 88  LEAGIGMVHQ-HFTLAENLTG--LENIVLGTESLFARKFSRSKARAKLQELMQSSGLE-- 142

Query: 386 QIKTTSLELPVASMSGGNQQKVVLAKCLSTEPVCLLCDEPTRGIDEGAKQEIYHLLDQFV 445
                 L+L V+ ++ G +Q+V + K L  +   L+ DEPT  +       +++ L    
Sbjct: 143 ----VDLDLRVSKLAVGERQRVEILKALYRDARILVLDEPTAVLTPQESDSLFNTLKLLA 198

Query: 446 RGGGAAIVVSSEAPELLHLSDRIAVFKGGRLV 477
             G A I +S +  E+L  SDR+AV +GGR+V
Sbjct: 199 AKGMAIIFISHKMAEVLGASDRVAVLRGGRIV 230


Lambda     K      H
   0.319    0.135    0.381 

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: 532
Number of extensions: 29
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: 495
Length of database: 515
Length adjustment: 34
Effective length of query: 461
Effective length of database: 481
Effective search space:   221741
Effective search space used:   221741
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