Alignments for a candidate for PS417_12065 in Collimonas arenae Ter10

GapMind for catabolism of small carbon sources

Alignments for a candidate for PS417_12065 in Collimonas arenae Ter10

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_061533691.1 CAter10_RS12710 sugar ABC transporter ATP-binding protein

Query= uniprot:A0A1N7TX47
         (495 letters)



>NCBI__GCF_001584165.1:WP_061533691.1
          Length = 516

 Score =  329 bits (844), Expect = 1e-94
 Identities = 190/471 (40%), Positives = 276/471 (58%), Gaps = 6/471 (1%)

Query: 7   LQAEHVAKAYAGVPALRDGRLSLRAGSVHALCGGNGAGKSTFLSILMGITQRDAGSILLN 66
           L+   + KA+ GV AL D  L L  G VH L G NGAGKST + +L G+   + G+I LN
Sbjct: 20  LELNGIYKAFGGVKALSDVSLRLYPGEVHTLMGQNGAGKSTLIKVLTGVHIPEHGTIRLN 79

Query: 67  GAPVQFNRPSEALAAGIAMITQELEPIPYMTVAENIWLGREPRRAGCIVDNKALNRRTRE 126
           G  V+     EA   GI+ + QE+   P ++VAENI++GR P + G I D K + R+ + 
Sbjct: 80  GREVRPTSTLEAQHLGISTVYQEVNLCPNLSVAENIFIGRYPTKFGAI-DWKTMQRQAQR 138

Query: 127 LLDSLEFDVDATSPMHRLSVAQIQLVEIAKAFSHDCQVMIMDEPTSAIGEHEAQTLFKAI 186
           LL  L+ D+D T+P+ R  +A  Q+V I++A S   +V+I+DEPTS++ E E Q LF  +
Sbjct: 139 LLGDLQIDIDVTAPLSRYPLAIQQMVAISRALSVSAKVLILDEPTSSLDEAEVQLLFSVL 198

Query: 187 RRLTAQGAGIVYVSHRLSELAQIADDYSIFRDGAFVESGRMADIDRDHLVRGIVGQ---- 242
           R+L  QG  I++V+H L +   I+D  ++ R+G      R+ ++ R  LV  +VG     
Sbjct: 199 RKLREQGMAILFVTHFLEQTYDISDRITVLRNGVLEGEYRVDELTRLELVNKMVGSQMQS 258

Query: 243 ELTRIDHKVGRECAANTCLQVDNLSRAGEFHDISLQLRQGEILGIYGLMGSGRSEFLNCI 302
           E+   D   G    A   LQ   L R G    + L LR GE+ G+ GL+GSGR+E    +
Sbjct: 259 EVQAPDAATGLRDNAEIVLQARGLGRKGILAPLDLDLRAGEVYGLCGLLGSGRTETARLL 318

Query: 303 YGLTVADSGSVTLQGKPM-PIGLPKATINAGMSLVTEDRKDSGLVLTGSILSNIALSAYK 361
           +G   ADSG+++++ KP+   G P+  I AG+   +EDRK  G +L  S+  NI L    
Sbjct: 319 FGADKADSGAISIKDKPLGKFGSPREAIAAGIGFCSEDRKQEGAILELSVRENIILGLQA 378

Query: 362 RLSSWSLINARKETQLAEDMVKRLQIKTTSLELPVASMSGGNQQKVVLAKCLSTEPVCLL 421
           R     +I  +++  +A D VK L IKT  +E P++S+SGGNQQK +LA+ L+T+PV L+
Sbjct: 379 RAGLLRVIPRKRQQAIAADYVKWLGIKTPDIETPISSLSGGNQQKALLARWLATDPVILI 438

Query: 422 CDEPTRGIDEGAKQEIYHLLDQFVRGGGAAIVVSSEAPELLHLSDRIAVFK 472
            DEPTRGID  AKQEI   +    R G A + +SSE  E+L  SDR+ V +
Sbjct: 439 LDEPTRGIDVRAKQEIMDHVIALCRKGMAILFISSEISEVLRCSDRMLVLR 489



 Score = 88.6 bits (218), Expect = 5e-22
 Identities = 70/248 (28%), Positives = 129/248 (52%), Gaps = 18/248 (7%)

Query: 5   LLLQAEHVAKAYAGVPALRDGRLSLRAGSVHALCGGNGAGKSTFLSILMGITQRDAGSIL 64
           ++LQA  + +   G+ A  D  L LRAG V+ LCG  G+G++    +L G  + D+G+I 
Sbjct: 275 IVLQARGLGRK--GILAPLD--LDLRAGEVYGLCGLLGSGRTETARLLFGADKADSGAIS 330

Query: 65  LNGAPV-QFNRPSEALAAGIAMITQELEP---IPYMTVAENIWLGREPRRAGCIVDNKAL 120
           +   P+ +F  P EA+AAGI   +++ +    I  ++V ENI LG + R AG +   + +
Sbjct: 331 IKDKPLGKFGSPREAIAAGIGFCSEDRKQEGAILELSVRENIILGLQAR-AGLL---RVI 386

Query: 121 NRRTRELL--DSLEF----DVDATSPMHRLSVAQIQLVEIAKAFSHDCQVMIMDEPTSAI 174
            R+ ++ +  D +++      D  +P+  LS    Q   +A+  + D  ++I+DEPT  I
Sbjct: 387 PRKRQQAIAADYVKWLGIKTPDIETPISSLSGGNQQKALLARWLATDPVILILDEPTRGI 446

Query: 175 GEHEAQTLFKAIRRLTAQGAGIVYVSHRLSELAQIADDYSIFRDGAFVESGRMADIDRDH 234
                Q +   +  L  +G  I+++S  +SE+ + +D   + RD          ++D D 
Sbjct: 447 DVRAKQEIMDHVIALCRKGMAILFISSEISEVLRCSDRMLVLRDREPCGEYLRGELDDDS 506

Query: 235 LVRGIVGQ 242
           +++ I G+
Sbjct: 507 VLQVIAGE 514



 Score = 72.8 bits (177), Expect = 3e-17
 Identities = 52/203 (25%), Positives = 100/203 (49%), Gaps = 6/203 (2%)

Query: 274 DISLQLRQGEILGIYGLMGSGRSEFLNCIYGLTVADSGSVTLQGKPMPIGLPKATINAGM 333
           D+SL+L  GE+  + G  G+G+S  +  + G+ + + G++ L G+ +    P +T+ A  
Sbjct: 37  DVSLRLYPGEVHTLMGQNGAGKSTLIKVLTGVHIPEHGTIRLNGREVR---PTSTLEAQH 93

Query: 334 SLVTEDRKDSGLVLTGSILSNIALSAYKRLSSWSLINARKETQLAEDMVKRLQIKTTSLE 393
             ++   ++  L    S+  NI +  Y   + +  I+ +   + A+ ++  LQI    + 
Sbjct: 94  LGISTVYQEVNLCPNLSVAENIFIGRYP--TKFGAIDWKTMQRQAQRLLGDLQIDI-DVT 150

Query: 394 LPVASMSGGNQQKVVLAKCLSTEPVCLLCDEPTRGIDEGAKQEIYHLLDQFVRGGGAAIV 453
            P++      QQ V +++ LS     L+ DEPT  +DE   Q ++ +L +    G A + 
Sbjct: 151 APLSRYPLAIQQMVAISRALSVSAKVLILDEPTSSLDEAEVQLLFSVLRKLREQGMAILF 210

Query: 454 VSSEAPELLHLSDRIAVFKGGRL 476
           V+    +   +SDRI V + G L
Sbjct: 211 VTHFLEQTYDISDRITVLRNGVL 233


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: 541
Number of extensions: 24
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: 495
Length of database: 516
Length adjustment: 34
Effective length of query: 461
Effective length of database: 482
Effective search space:   222202
Effective search space used:   222202
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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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 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