Alignments for a candidate for deh in Sinorhizobium meliloti 1021

GapMind for catabolism of small carbon sources

Alignments for a candidate for deh in Sinorhizobium meliloti 1021

Align Acetate/haloacid transporter, Dehp2, with a possible atypical topology (characterized)
to candidate SMc04407 SMc04407 transport transmembrane protein

Query= TCDB::F8SVK1
         (552 letters)



>FitnessBrowser__Smeli:SMc04407
          Length = 629

 Score =  576 bits (1485), Expect = e-169
 Identities = 291/440 (66%), Positives = 348/440 (79%), Gaps = 3/440 (0%)

Query: 5   SGQISHAPMTKEEKRVIFASSLGTVFEWYDFYLAGSLAAFISKSFFSGVNPTAAFIFTLL 64
           +G     PMT EEK+VIFASSLGTVFEWYDFYL GSLA +I  +FFS    T   IF LL
Sbjct: 7   AGGTKAGPMTGEEKKVIFASSLGTVFEWYDFYLYGSLAVYIGATFFSQYPETTRNIFALL 66

Query: 65  GFAAGFAVRPFGALVFGRLGDMVGRKYTFLITIVIMGLSTCVVGFLPGYAAIGMASPVIF 124
            FAAGF VRPFGALVFGRLGD+VGRKYTFL+TI+IMG+ST +VG LPG A+IG+A+P+I 
Sbjct: 67  AFAAGFLVRPFGALVFGRLGDLVGRKYTFLVTILIMGVSTFLVGVLPGAASIGIAAPIIL 126

Query: 125 IAMRLLQGLALGGEYGGAATYVAEHAPANRRGFYTAWIQTTATLGLFLSLLVILGVRTAM 184
           IA+RLLQGLALGGEYGGAATYVAEHAP  RRG++T+WIQTTATLGLFLSL+VIL V+  +
Sbjct: 127 IALRLLQGLALGGEYGGAATYVAEHAPHGRRGYFTSWIQTTATLGLFLSLVVILLVQYML 186

Query: 185 GEDAFGAWGWRIPFVASLVLLGISVWIRMQLHESPAFERIKAEGKTSKAPLSEAFGQWKN 244
           G++AF  WGWRIPF+ S VLLG+SVWIR++++ESPAF+++K EGK SKAPL+EAFGQW+N
Sbjct: 187 GKEAFAEWGWRIPFLLSFVLLGVSVWIRLKMNESPAFKKMKEEGKGSKAPLTEAFGQWRN 246

Query: 245 LKIVILALIGVTAGQAVVWYTGQFYALFFLTQTLKVDGASANILIAIALLIGTPFFLFFG 304
            KI +LAL G   GQAVVWY+GQFYALFFL   LKVDG SAN+++A +LL+GT FF+FFG
Sbjct: 247 AKIAVLALFGAVVGQAVVWYSGQFYALFFLQSILKVDGQSANLMVAASLLLGTGFFVFFG 306

Query: 305 SLSDRIGRKPIILAGCLIAALTYFPLFKALTHYANPALEAATQKSPIVVIANPDECSFQF 364
            LSD+IGRKPII+AG L+A LTYFPLFKALT   NPAL  A Q     V A P +C FQF
Sbjct: 307 WLSDKIGRKPIIMAGLLLAMLTYFPLFKALTWAGNPALAEAQQSVRATVTAAPGDCKFQF 366

Query: 365 NPVGTSKFTSSCDIAKSALSKAGLNYDNV-AAPAGTLAQIKVGDTTIDTYDGKAAD--AK 421
           NP GT+KFT+SCDIA + L+K  + YD V  A AGT A +K+G+TTI +YD  AA   AK
Sbjct: 367 NPTGTAKFTTSCDIATAFLTKNSVPYDVVTTAAAGTPATVKIGETTITSYDAIAAGDRAK 426

Query: 422 DAGKAFDKNLGTALKAASYP 441
               AF K +  AL+A+ YP
Sbjct: 427 AEEAAFGKQINMALQASGYP 446



 Score =  178 bits (452), Expect = 5e-49
 Identities = 87/156 (55%), Positives = 113/156 (72%), Gaps = 4/156 (2%)

Query: 401 AQIKVGDTTIDTYDGKAADA----KDAGKAFDKNLGTALKAASYPPKADPSQLNWPMTVV 456
           A ++ G+ T+   D   AD     ++ G A +  +    K  ++   ADP+++NW + + 
Sbjct: 474 AAVRAGEKTMVPADKLVADKLLTQEEVGSATEMAVYNIDKGGAFTMVADPARVNWTVIIA 533

Query: 457 ILTILVIYVTMVYGPIAAMLVEMFPTRIRYTSMSLPYHIGNGWFGGFLPATAFAIVAAKG 516
           +LT+LVIYVTMVYGPIAA+LVE+FPTRIRYT MSLPYHIGNGWFGG LPATAFA+ AAKG
Sbjct: 534 VLTVLVIYVTMVYGPIAALLVELFPTRIRYTGMSLPYHIGNGWFGGLLPATAFAMSAAKG 593

Query: 517 NIYSGLWYPIIIALATFVIGLLFVRETKDSNIYAQD 552
           +IY GLWYPI+ A  T VIGLLF+ ETKD +I+  +
Sbjct: 594 DIYYGLWYPIVFAGITLVIGLLFLPETKDRDIHTME 629


Lambda     K      H
   0.325    0.139    0.422 

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: 954
Number of extensions: 33
Number of successful extensions: 4
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: 629
Length adjustment: 37
Effective length of query: 515
Effective length of database: 592
Effective search space:   304880
Effective search space used:   304880
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: 53 (25.0 bits)

This GapMind analysis is from Sep 17 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