GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dctM in Sinorhizobium meliloti 1021

Align C4-dicarboxylate TRAP transporter large permease protein DctM (characterized)
to candidate SM_b21351 SM_b21351 C4-dicarboxylate large membrane transport protein

Query= SwissProt::O07838
         (440 letters)



>FitnessBrowser__Smeli:SM_b21351
          Length = 427

 Score =  300 bits (767), Expect = 8e-86
 Identities = 151/435 (34%), Positives = 257/435 (59%), Gaps = 13/435 (2%)

Query: 1   MSALIIFGLLIALMLTGMPISISLGLTVLTFLFTMTQVPIDTVALKLFTGIEKFEIMAIP 60
           M  +I+FG+   LML G PI+  LG+     +  +   P+  +  +L +G+  F ++AIP
Sbjct: 1   MDMMILFGVFTLLMLIGTPIAFCLGVASFATVLYLGLPPL-VIFQRLNSGMSVFSLLAIP 59

Query: 61  FFILAGNFLTHGGVAKRMINFATAMVGHWHGGLGLAGVIACALFAAVSGSSPATVVAIGS 120
           FFI AG+ +  GG+A++++ FA ++VGH  GGLG   ++   LF  +SGS+ A   A+G 
Sbjct: 60  FFIYAGDLMVRGGIAQKIVAFAASLVGHIRGGLGQVNIVTATLFGGISGSAVAEAAAVGG 119

Query: 121 VILPAMVNQGFPKQFGAGVITTSGALGILIPPSIVMVMYAVATSGMVVTGPDGQPVSSAS 180
           +++P M  +G+   +   V + +  + +++PPS  M++Y+++  G +            S
Sbjct: 120 LMIPQMKQRGYGADYAVNVTSMAALIALMLPPSHNMIIYSISAGGKI------------S 167

Query: 181 VGELFMAGVVPGLMLAGFLAFTTWNRARKFGYPRLEKASLRQRWTAFREAAWGLMLIVVV 240
           + +LF AG++PGL+ A  L  T +  AR+ GYP        +       +  GL+LI ++
Sbjct: 168 IADLFTAGILPGLLYAAALMATAYFVARRRGYPTEVFPGFARVGRYLLISTPGLLLIGII 227

Query: 241 IGGIYAGIFTPTEAAAMSAVYAFFISVFVYKDLTLRDVPRVLLSSANMSAMLLYIITNAV 300
            GG+ +G+FT TE++ ++ +YA  ++VFVY+ +T +D  +   ++   +AM+L II  A 
Sbjct: 228 FGGVRSGVFTATESSCIAVLYALAVTVFVYRQMTWQDFVQATFAAVRTTAMVLLIIGMAA 287

Query: 301 LFSFLMAHEGIPQALGEWMVNAGLSWWMFLIIVNILLLAAGNFMEPSSIVLIMAPILFPV 360
            FS+LMA   +P AL +WM     +  + L+++N+L+L  G FM+    ++I  PI  PV
Sbjct: 288 AFSWLMAFLRVPAALIDWMNTISENPIIILLLLNVLMLFLGTFMDMGPTIIICTPIFLPV 347

Query: 361 AVRLGIDPVHFGIMIVVNMEVGMCHPPVGLNLYVASGITKMGITELTVAVWPWLLTMLAF 420
           A+  G+DPVHFG+++++N  +G+  PPVG   +VA  + K+ + E   ++WP+ L  L  
Sbjct: 348 AMAYGVDPVHFGVIMILNFGIGLNTPPVGAVQFVACAVGKISVWEAMRSIWPFYLAGLIV 407

Query: 421 LVLVTYVPAISLALP 435
           L LVTYVPA+SL LP
Sbjct: 408 LGLVTYVPALSLWLP 422


Lambda     K      H
   0.329    0.142    0.431 

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: 585
Number of extensions: 33
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 440
Length of database: 427
Length adjustment: 32
Effective length of query: 408
Effective length of database: 395
Effective search space:   161160
Effective search space used:   161160
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 51 (24.3 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:

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:

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:

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:

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