GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dctM in Cupriavidus basilensis 4G11

Align dicarboxylate TRAP transporter (succinate, fumarate, L-malate, and alpha-ketoglutarate), large permease component (characterized)
to candidate RR42_RS06530 RR42_RS06530 C4-dicarboxylate ABC transporter

Query= reanno::PV4:5208943
         (465 letters)



>FitnessBrowser__Cup4G11:RR42_RS06530
          Length = 434

 Score =  221 bits (563), Expect = 4e-62
 Identities = 144/467 (30%), Positives = 237/467 (50%), Gaps = 55/467 (11%)

Query: 6   LFISLFLCMLLGMPIAIALGFSSMLTILLFSDDS----LASVALKLYESTSEHYTLLAIP 61
           LF+     M+LG+PI ++LG   ++ I L + D+    L +V    Y    + Y LLAIP
Sbjct: 8   LFVVFLGLMMLGVPIGVSLGLGGLVAIGLSNLDTQMFGLLAVPQNFYAGLGK-YPLLAIP 66

Query: 62  FFILSSAFLSTGGVARRIIDFAMDSVGHIRGGLAMASVMACMLFAAVSGSSPATVAAIGS 121
            F+L  +     GVA+R++ FA+  VG   G L + +++  M    +SGS PA  AA+G 
Sbjct: 67  MFVLVGSIFDRSGVAQRLVTFAIAIVGRGPGMLPLVAILVAMFLGGISGSGPANAAAVGG 126

Query: 122 IVIVGMVRAGYPEKFAAGVITTSGTLGILIPPSIVMLVYAAATE-VSAARMFMAGLIPGL 180
           ++I  M RAGYP  ++A V+  +    ILIPPS+  ++Y+      S   +F AG+IPG+
Sbjct: 127 VMIAAMSRAGYPGAYSAAVVGAAAATDILIPPSVAFIIYSVLVPGASVPALFAAGMIPGI 186

Query: 181 MMGLLLMLAIYIVARIKKL----PSRPFPGFRPLAISSAKAMGGLALIVIVLGSIYGGIA 236
           + G+ L++    +AR   +       P P   P   S  +A  GL    ++LG +  G  
Sbjct: 187 LAGVALIVPAVWLARKHNMGAIEAGLPRP---PFWKSLREAAWGLVAPFLILGGMRAGWF 243

Query: 237 SPTEAAAVACVYAYFIAVFGYRDIGPLKNVSWRDSGEPLIRAILRNLGFMVLAVFKTPAD 296
           +PTEAA VA VY  F+ +  YR      ++S RD                +  +F     
Sbjct: 244 TPTEAAVVAVVYGLFVGMVIYR------SISMRD----------------LFVIF----- 276

Query: 297 KEIRHVVRDGAKVSIMLLFIIANAMLFAHVLTTERIPHLIAETIVGMGLPVWGFLIIVNL 356
                  ++ A+ S ++L ++A A +FA+ L+T  +   +A  I   GL  +G L ++  
Sbjct: 277 -------QEAAETSAVILLVVALAGIFAYALSTLGVIDPLANAIAHSGLGEYGVLALIVA 329

Query: 357 LLLAAGNFMEPSAILLIMAPILFPIATQLGIDPIHLGIIMVVNMEIGMLTPPVGLNLFVT 416
           LL+  G F++  +I LI  P+L PIA     +P+  G+++ + + +G  TPP+ +NL V+
Sbjct: 330 LLMTVGMFLDGISIFLIFVPLLLPIANAFHWNPVWFGVVLTLKVALGQFTPPLAVNLMVS 389

Query: 417 AGITGRSMGWVIHSCIPWLA--LLLFFLA--LITYIPQISLFLPEYI 459
             I    M       +PW+   LL  F+A  L+   P ++ +LP+Y+
Sbjct: 390 CRIARVRM----EETVPWVVWMLLAMFVAMLLVLAFPPLATWLPDYL 432


Lambda     K      H
   0.330    0.144    0.424 

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: 639
Number of extensions: 44
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: 465
Length of database: 434
Length adjustment: 33
Effective length of query: 432
Effective length of database: 401
Effective search space:   173232
Effective search space used:   173232
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