Alignments for a candidate for deh in Flavobacterium ummariense DS-12

GapMind for catabolism of small carbon sources

Alignments for a candidate for deh in Flavobacterium ummariense DS-12

Align The acetate/monochloroacetate (haloacid) permease, Deh4p (Km = 5.5 mμM for acetate; 9 mμM for monochloroacetate) (characterized)
to candidate WP_091521441.1 BM253_RS07155 MHS family MFS transporter

Query= TCDB::Q7X4L6
         (552 letters)



>NCBI__GCF_900115115.1:WP_091521441.1
          Length = 514

 Score =  496 bits (1276), Expect = e-144
 Identities = 261/529 (49%), Positives = 345/529 (65%), Gaps = 42/529 (7%)

Query: 20  VIFASSLGTVFEWYDFYLAGSLAIYISRTFFSGVNPAAGFVFTLLGFAAGFAVRPFGAIV 79
           VI ASS+GT+ EWYDFY+ GSLAI +S  FF   NP A F+ TL  FAAGF VRPFGA+ 
Sbjct: 14  VIMASSMGTLIEWYDFYIFGSLAIVLSTKFFPSDNPTAAFLSTLATFAAGFVVRPFGALF 73

Query: 80  FGRLGDMIGRKYTFLATILLMGLSTFVVGLLPGYGTIGMTAPVVFIAMRMLQGLALGGEY 139
           FGRLGD+IGRKYTF+ T++LMG +TFV+G +P Y +IG  APV+ + MR+LQGLALGGEY
Sbjct: 74  FGRLGDLIGRKYTFMVTLMLMGGATFVIGCVPSYESIGFVAPVIVLVMRLLQGLALGGEY 133

Query: 140 GGAATYVAEHAPSNKRGAWTAWIQTTATLGLFISLLVILSVRSLLNEDTFAAWGWRVPFL 199
           GGAATYVAEHAP  +RG WT+WIQTTAT+GLFISL+VIL  RS++ E+ F  WGWRVPF 
Sbjct: 134 GGAATYVAEHAPKGQRGFWTSWIQTTATVGLFISLIVILITRSVMTEEQFDLWGWRVPFW 193

Query: 200 VSIVLLAVSVWIRMQLHESPVFERIKAEGKTSKAPLSEAFGQWKNLKIVLLALFGLTAGQ 259
           +SIV++ +S  IR  + ESP F + K EGKTS  PL E+FG   NLK VLLALFG T GQ
Sbjct: 194 LSIVMVYISYLIRKNMSESPEFAKAKKEGKTSTNPLKESFGNRYNLKFVLLALFGATMGQ 253

Query: 260 AVVWYTGQFYTLFFLTQTLKVDGTSANMLVAVALLIGTPFFLFFGSLSDKIGRKPIIMAG 319
            V+WYTGQFY + ++   + VD    + L+ +ALL+GTPFF+FFG LSDK+GRKPI++AG
Sbjct: 254 GVIWYTGQFYAMSYIKTVMFVDSNQVDGLLGIALLLGTPFFVFFGWLSDKVGRKPILLAG 313

Query: 320 CLIAALTYFPLFKALAHYTNPKLEAATLQAPITMIADPSECSFQFNPVGTAKFTSSCDVA 379
            LIA ++Y P+++A+   T+  L+        T + D    S +           + + A
Sbjct: 314 MLIAIISYRPIYRAMYASTDTNLK--------TEMVDKRIASAEI---------KTTNAA 356

Query: 380 KGALSKAGLNYENITAPAGTVAQIRIGDKVVDAYDGKAADAKARGAEFEQTLSKSLETAG 439
             ++ K    Y + T  + T   + + D V +  +    D   +   F   ++ S     
Sbjct: 357 SDSIYKVKKFYTDGTEYSETTT-VHLKDGVANITEKGDVDKHVKKTMF---ITSS----- 407

Query: 440 YPAKADPALINWPMSILILTILVLYVTMVYGPLAAMLVEMFPARIRYTSMSLPYHIGNGW 499
                    I W +  L+  + VL+VTMVYGP+AA LVEMFP +IRYTSMSLPYHIGNG 
Sbjct: 408 ---------IKWKLVFLVF-VQVLFVTMVYGPIAAFLVEMFPVKIRYTSMSLPYHIGNGI 457

Query: 500 FGGFLPATAFAIIAARGN------IYSGLWYPIVIASVAFVIGTLFVKE 542
           FGG LPA +   +A             GLWYPI++ +++FVIG +++ +
Sbjct: 458 FGGLLPAISTYFVANAEKTGHSEFFLEGLWYPIIVGAISFVIGFIYINK 506


Lambda     K      H
   0.325    0.139    0.420 

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: 723
Number of extensions: 24
Number of successful extensions: 5
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: 552
Length of database: 514
Length adjustment: 35
Effective length of query: 517
Effective length of database: 479
Effective search space:   247643
Effective search space used:   247643
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 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 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