GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ytfR in Desulfovibrio vulgaris Hildenborough

Align galactofuranose ABC transporter putative ATP binding subunit (EC 7.5.2.9) (characterized)
to candidate 206505 DVU1070 branched chain amino acid ABC transporter, ATP-binding protein

Query= ecocyc::YTFR-MONOMER
         (500 letters)



>MicrobesOnline__882:206505
          Length = 524

 Score =  227 bits (579), Expect = 7e-64
 Identities = 152/478 (31%), Positives = 247/478 (51%), Gaps = 29/478 (6%)

Query: 9   ILRTEGLSKFFPGVKALDNVDFSLRRGEIMALLGENGAGKSTLIKALTGVYHADRGTIWL 68
           ++R EG+ K F  V+A  ++   +  G I ALLGENGAGKSTL+  L+G    D G I +
Sbjct: 34  VVRLEGIGKSFGPVRANHDITLDIVPGRIKALLGENGAGKSTLMSILSGRLAQDTGIIHV 93

Query: 69  EGQAISPKNTAHAQQLGIGTVYQEVNLLPNMSVADNLFIGREPKRFGLLRRKEMEKRATE 128
           +G+A+  ++   A + GIG VYQ   L+ +M+VA+N+ +G+       L    M +   E
Sbjct: 94  DGEAVRFRSPKDALKAGIGMVYQHFMLVDSMTVAENVLLGQSG---AWLSPVHMSRVVAE 150

Query: 129 LMASYGFSLDVREPLNRFSVAMQQIVAICRAIDLSAKVLILDEPTASLDTQEVELLFDLM 188
           L A YG  +D    +   S+  +Q V I + +   ++VLILDEPTA L   E E LF+ +
Sbjct: 151 LAARYGLDIDPAARVCDLSMGERQRVEILKLLYRDSRVLILDEPTAVLTPGETEQLFEAL 210

Query: 189 RQLRDRGVSLIFVTHFLDQVYQVSDRITVLRNGSFVGCRETCELP-QIELVKMMLGR--- 244
            ++ + G +++F++H + +V  ++D I +LR G  V      E+P + EL   M+GR   
Sbjct: 211 HRMAENGKAIVFISHKMQEVLALADEIAILRRGEVVDEFHESEVPGEAELANRMVGREVI 270

Query: 245 -ELDTHALQRAGRTLLSDKPVAAFKNYGKKGTIAPFDLEVRPGEIVGLAGLLGSGRTETA 303
            E+    L+   R L  D         G KG       EVR GE+  +AG+ G+G+ E  
Sbjct: 271 LEVAAEPLEPGDRVLHVD----GLAGDGLKG----LSFEVRKGEVFAIAGVAGNGQRELV 322

Query: 304 EVIFGIKPADSGTALIKGKPQN---LRSPHQASVLGIGFCPEDRKTDGIIAAASVRENII 360
           E + G++    G   + G P      ++P Q    G+ + PEDR+      +  + +N +
Sbjct: 323 ECVTGLRRPAEGEVELLGIPWRQFFTKAPRQG---GLAYIPEDRQGLATCLSLDLVDNFL 379

Query: 361 LALQA--QRGWLRPISRKEQQEIAERFIRQLGIRTPSTEQPIEFLSGGNQQKVLLSRWLL 418
           L  +    RG    + RK     A   + +  ++    E P   LSGGN QK+++ R   
Sbjct: 380 LTARGCFTRGPF--LDRKSADAAARDILAEYNVQPGRAEAPARSLSGGNLQKLVVGREFY 437

Query: 419 TRPQFLILDEPTRGIDVGAHAEI-IRLIETLCADGLALLVISSELEELVGYADRVIIM 475
            +P  ++ + PT+G+D+ A  E+  RL+E     G  +L++S +L E++  ADRV +M
Sbjct: 438 RKPSLIVAENPTQGLDIAATEEVWARLLEVRSHAG--VLLVSGDLNEVLALADRVAVM 493



 Score = 80.1 bits (196), Expect = 2e-19
 Identities = 66/243 (27%), Positives = 114/243 (46%), Gaps = 16/243 (6%)

Query: 253 RAGRTLLSD-KPVAAFKNYGKK-GTIAP---FDLEVRPGEIVGLAGLLGSGRTETAEVIF 307
           R GR L  D  PV   +  GK  G +       L++ PG I  L G  G+G++    ++ 
Sbjct: 22  RTGRALRHDVTPVVRLEGIGKSFGPVRANHDITLDIVPGRIKALLGENGAGKSTLMSILS 81

Query: 308 GIKPADSGTALIKGKPQNLRSPHQASVLGIGFCPEDRKTDGIIAAASVRENIILALQAQR 367
           G    D+G   + G+    RSP  A   GIG   +      ++ + +V EN++L      
Sbjct: 82  GRLAQDTGIIHVDGEAVRFRSPKDALKAGIGMVYQHFM---LVDSMTVAENVLLGQSG-- 136

Query: 368 GWLRPISRKEQ-QEIAERFIRQLGIRTPSTEQPIEFLSGGNQQKVLLSRWLLTRPQFLIL 426
            WL P+       E+A R+    G+      +  + LS G +Q+V + + L    + LIL
Sbjct: 137 AWLSPVHMSRVVAELAARY----GLDIDPAARVCD-LSMGERQRVEILKLLYRDSRVLIL 191

Query: 427 DEPTRGIDVGAHAEIIRLIETLCADGLALLVISSELEELVGYADRVIIMRDRKQVAEIPL 486
           DEPT  +  G   ++   +  +  +G A++ IS +++E++  AD + I+R  + V E   
Sbjct: 192 DEPTAVLTPGETEQLFEALHRMAENGKAIVFISHKMQEVLALADEIAILRRGEVVDEFHE 251

Query: 487 AEL 489
           +E+
Sbjct: 252 SEV 254



 Score = 65.9 bits (159), Expect = 3e-15
 Identities = 54/240 (22%), Positives = 110/240 (45%), Gaps = 12/240 (5%)

Query: 9   ILRTEGLSKFFPGVKALDNVDFSLRRGEIMALLGENGAGKSTLIKALTGVYHADRGTIWL 68
           +L  +GL+    G+K L    F +R+GE+ A+ G  G G+  L++ +TG+     G + L
Sbjct: 284 VLHVDGLAG--DGLKGLS---FEVRKGEVFAIAGVAGNGQRELVECVTGLRRPAEGEVEL 338

Query: 69  EGQAISPKNTAHAQQLGIGTVYQEVNLLP---NMSVADNLFIGREP--KRFGLLRRKEME 123
            G       T   +Q G+  + ++   L    ++ + DN  +       R   L RK  +
Sbjct: 339 LGIPWRQFFTKAPRQGGLAYIPEDRQGLATCLSLDLVDNFLLTARGCFTRGPFLDRKSAD 398

Query: 124 KRATELMASYGFSLDVRE-PLNRFSVAMQQIVAICRAIDLSAKVLILDEPTASLDTQEVE 182
             A +++A Y       E P    S    Q + + R       +++ + PT  LD    E
Sbjct: 399 AAARDILAEYNVQPGRAEAPARSLSGGNLQKLVVGREFYRKPSLIVAENPTQGLDIAATE 458

Query: 183 LLFDLMRQLRDRGVSLIFVTHFLDQVYQVSDRITVLRNGSFVGCRETCELPQIELVKMML 242
            ++  + ++R     ++ V+  L++V  ++DR+ V+  G F+G  +  +  +++ + +M+
Sbjct: 459 EVWARLLEVRSHA-GVLLVSGDLNEVLALADRVAVMYRGCFIGLLDRSDTNKVDAIGLMM 517


Lambda     K      H
   0.321    0.138    0.391 

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: 599
Number of extensions: 35
Number of successful extensions: 8
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: 500
Length of database: 524
Length adjustment: 35
Effective length of query: 465
Effective length of database: 489
Effective search space:   227385
Effective search space used:   227385
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 17 2021. The underlying query database was built on Sep 17 2021.

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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