Alignments for a candidate for ytfR in Desulfovibrio oxyclinae DSM 11498

GapMind for catabolism of small carbon sources

Alignments for a candidate for ytfR in Desulfovibrio oxyclinae DSM 11498

Align galactofuranose ABC transporter putative ATP binding subunit (EC 7.5.2.9) (characterized)
to candidate WP_156816733.1 B149_RS0103930 ABC transporter ATP-binding protein

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



>NCBI__GCF_000375485.1:WP_156816733.1
          Length = 510

 Score =  220 bits (560), Expect = 1e-61
 Identities = 155/485 (31%), Positives = 249/485 (51%), Gaps = 28/485 (5%)

Query: 5   QHQEILRTEGLSKFFPGVKALDNVDFSLRRGEIMALLGENGAGKSTLIKALTGVYHADRG 64
           ++  +L   G++K F  V A  ++ F +R G++ ALLGENGAGKSTL+  + G +  D G
Sbjct: 3   ENAPLLSCRGVTKRFGEVVANRDITFEVRAGQVQALLGENGAGKSTLMSVIAGRFRPDAG 62

Query: 65  TIWLEGQAISPKNTAHAQQLGIGTVYQEVNLLPNMSVADNLFIGREPKRFGLLRRKEMEK 124
            I + G+ +     A A ++GIG VYQ   L+  ++VA+N+ +       G    ++ ++
Sbjct: 63  EIRVRGELVQFSRPADAMRMGIGMVYQRFMLVERLTVAENIRLSAHSCGIG---SRQADR 119

Query: 125 RATELMASYGFSLDVREPLNRFSVAMQQIVAICRAIDLSAKVLILDEPTASLDTQEVELL 184
           R  EL   YG  +D    +   S+  +Q   I + +  +A +LI DEPTA L   E E L
Sbjct: 120 RMAELSERYGLGVDPSRTVGSLSMGERQRAEILKLLVQNANILIFDEPTAVLSQPEAEGL 179

Query: 185 FDLMRQLRDRGVSLIFVTHFLDQVYQVSDRITVLRNGSFVGCRETCEL-PQIELVKMMLG 243
           F +  +LR  G  ++F+TH L++V   +D I++LR G  +      E+  + EL ++M+G
Sbjct: 180 FKIFDRLRQNGCGVVFITHKLEEVMAAADHISILRRGRIIASVAPGEIESKRELARLMVG 239

Query: 244 RE----LDTHALQRAGRTLLSDKPVAAFKNYGKKGTIAPFDLEVRPGEIVGLAGLLGSGR 299
           RE    +D   L   G T+L  K  A     G+ G     +L VR GEI+ + G+ G+G+
Sbjct: 240 REFVLAVDKPEL-NPGETVLELKHFAGSGASGRTG-FEGVNLSVRRGEILAVIGVAGNGQ 297

Query: 300 TETAEVIFGIKPADSGTA---LIKGKPQNLRSPHQASVLGIGFCPEDRKTDGIIAAASVR 356
           +  A  + G    D+G A    +    + + +P      GI   PEDR   G +   ++ 
Sbjct: 298 SALAAAVTG--NTDAGLAESGSVTFGDETVSAPDWKGHHGIAHVPEDRHNTGSVHDMTLA 355

Query: 357 ENIILALQAQRG---W--LRPISRKEQQEIAERFIRQLGIRTPSTEQPIEFLSGGNQQKV 411
           EN  L      G   W  L  I++K Q+ I    IR  G      E     LSGGN QK+
Sbjct: 356 ENYALTRLDAAGDGPWFDLSRIAKKTQKAIENYSIRATG-----AEDMAGSLSGGNLQKL 410

Query: 412 LLSRWLLTRPQFLILDEPTRGIDVGAHAEI-IRLIETLCADGLALLVISSELEELVGYAD 470
           +L+R L  +P+  + ++PT+G+D+ +  EI   LI      G  +L+ S +L+E++  AD
Sbjct: 411 ILARELARKPELFVAEQPTQGLDIASTEEIWAALIRQRKHSG--ILLFSGDLKEVLTLAD 468

Query: 471 RVIIM 475
           R+ +M
Sbjct: 469 RIAVM 473



 Score = 70.9 bits (172), Expect = 1e-16
 Identities = 57/222 (25%), Positives = 104/222 (46%), Gaps = 9/222 (4%)

Query: 268 KNYGKKGTIAPFDLEVRPGEIVGLAGLLGSGRTETAEVIFGIKPADSGTALIKGKPQNLR 327
           K +G+         EVR G++  L G  G+G++    VI G    D+G   ++G+     
Sbjct: 15  KRFGEVVANRDITFEVRAGQVQALLGENGAGKSTLMSVIAGRFRPDAGEIRVRGELVQFS 74

Query: 328 SPHQASVLGIGFCPEDRKTDGIIAAASVRENIILALQAQRGWLRPISRKEQQEIAERFIR 387
            P  A  +GIG   +      ++   +V ENI L+  +     R   R+   E++ER+  
Sbjct: 75  RPADAMRMGIGMVYQRFM---LVERLTVAENIRLSAHSCGIGSRQADRR-MAELSERY-- 128

Query: 388 QLGIRTPSTEQPIEFLSGGNQQKVLLSRWLLTRPQFLILDEPTRGIDVGAHAEIIRLIET 447
            LG+    T   +  LS G +Q+  + + L+     LI DEPT  +       + ++ + 
Sbjct: 129 GLGVDPSRT---VGSLSMGERQRAEILKLLVQNANILIFDEPTAVLSQPEAEGLFKIFDR 185

Query: 448 LCADGLALLVISSELEELVGYADRVIIMRDRKQVAEIPLAEL 489
           L  +G  ++ I+ +LEE++  AD + I+R  + +A +   E+
Sbjct: 186 LRQNGCGVVFITHKLEEVMAAADHISILRRGRIIASVAPGEI 227


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: 550
Number of extensions: 34
Number of successful extensions: 8
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: 500
Length of database: 510
Length adjustment: 34
Effective length of query: 466
Effective length of database: 476
Effective search space:   221816
Effective search space used:   221816
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 Apr 09 2024. 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 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