Alignments for a candidate for cbtF in Desulfuromonas acetexigens DSM 1397

GapMind for catabolism of small carbon sources

Alignments for a candidate for cbtF in Desulfuromonas acetexigens DSM 1397

Align CbtF, component of Cellobiose and cellooligosaccharide porter (characterized)
to candidate WP_092058281.1 BQ4888_RS15490 ABC transporter ATP-binding protein

Query= TCDB::Q97VF4
         (324 letters)



>NCBI__GCF_900111775.1:WP_092058281.1
          Length = 596

 Score =  129 bits (325), Expect = 1e-34
 Identities = 77/234 (32%), Positives = 129/234 (55%), Gaps = 6/234 (2%)

Query: 27  ALKDVSLSMNQGDLLIVLGESGAGKTTLGRVIVGLQKPTSGEVVYDGYNIWKNKRKIFKK 86
           AL  V L + QG++  ++GE+G+GK+TL  +  G  +P  G   + G ++    R+    
Sbjct: 355 ALAPVDLRLRQGEVFGLVGETGSGKSTLAMIAAGALRPDGGRRDFSGRDLEDWLRRDRLS 414

Query: 87  YRKDVQLIPQDPYSTLPFNKTVEEILVAPI-LRWEKINKDELRKRLINLLELVKLTPAEE 145
             + + ++ Q P   +     V  I+  P+ ++ +  + D LR+R+   L  V L  A E
Sbjct: 415 LARRIGIVQQHPALAVSPRFDVFGIVAEPLRIQGQTDSADVLRERVTRALVEVHLPTAPE 474

Query: 146 FLGKYPHQLSGGQKQRLSIARSLSVNPRIIVADEPVTMVDASLRIGILNTLAEIKNRLNL 205
           FL + PHQL+ G  QRL IAR+L   P +++ADEP + +D S++  IL  L +++    L
Sbjct: 475 FLRRLPHQLNQGALQRLCIARALITEPLLLIADEPTSALDPSVQAKILKLLLDLQIEKGL 534

Query: 206 TMVFITHDIPIARYFYHLFDKGNTIVMFAGRIVERADLEEILKDPLHPYTNDLI 259
           T++ +THD+ +AR            VM AGR+VE  +  ++L+ P HPYT +L+
Sbjct: 535 TLLLVTHDLGLARKVCDRIG-----VMHAGRLVEVGNAAQVLQRPAHPYTRELL 583



 Score =  105 bits (263), Expect = 2e-27
 Identities = 84/321 (26%), Positives = 145/321 (45%), Gaps = 41/321 (12%)

Query: 27  ALKDVSLSMNQGDLLIVLGESGAGKTTLGRVIVGLQKPTS---GEVVYDGYNIWKNKRKI 83
           AL  V L +  G +L ++GESG+GKTTL R ++GL    +   G V  DG  +       
Sbjct: 20  ALDRVDLRLEPGRVLALVGESGSGKTTLARSLLGLTDKNARIDGVVRLDGEELTGFSEGA 79

Query: 84  FKKYR-KDVQLIPQDPYSTLPFNKTVEEILVAPILRWEKINKDELRKRLINLLELVKLTP 142
           + + R   + ++ Q+  + L    ++   +  P++    +       +    L  + L P
Sbjct: 80  WNRVRWARIAMVGQNGAAALNPVLSIGAQVAEPLIEHRGLGSGAALAQAEMALTAMGLDP 139

Query: 143 AEEFLGKYPHQLSGGQKQRLSIARSLSVNPRIIVADEPVTMVDASLRIGILNTLAEIKNR 202
           A     +YPH+LSGGQ QR  +A +L ++P++++ DEP   +D   R  +   + + + R
Sbjct: 140 AAA--RRYPHELSGGQIQRALLAMALILDPQVLILDEPTAALDPPARQFVGEVIRD-QRR 196

Query: 203 LNLTMVFITHDIPIARYFYHLFDKGNTIVMFAGRIVERADLEEILKDPLHPYTNDLIKLT 262
               ++ I+HD+   R    L D+    V++ GRI+E     ++  +P HPYT  L++  
Sbjct: 197 RGKAILLISHDLDSCR---RLADR--VAVLYLGRILEELPARDLFANPCHPYTRALVRSY 251

Query: 263 PSIDNL-----------YKEINVK-----------------INYERVEKGCPYRLRCPFA 294
           P ID +           Y+ ++                    N    E+GC +  RC  A
Sbjct: 252 PRIDGVRDLGGMRGDAFYRMVHAHDRLAADHVHTMGSGDPGENGHAPERGCLFAPRCTQA 311

Query: 295 MDICKNEEPKLFKY-SHEVAC 314
              C+ EEP+L     H + C
Sbjct: 312 EAACREEEPELCSVGGHRLRC 332


Lambda     K      H
   0.321    0.141    0.410 

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: 457
Number of extensions: 31
Number of successful extensions: 7
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: 324
Length of database: 596
Length adjustment: 32
Effective length of query: 292
Effective length of database: 564
Effective search space:   164688
Effective search space used:   164688
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: 51 (24.3 bits)

This GapMind analysis is from Apr 09 2024. 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