Aligments for a candidate for ytfR in Desulfovibrio vulgaris Hildenborough

GapMind for catabolism of small carbon sources

Aligments 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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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 paper from 2022 on GapMind for carbon sources, or view the source code.

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