Alignments for a candidate for deh in Cupriavidus basilensis 4G11

GapMind for catabolism of small carbon sources

Alignments for a candidate for deh in Cupriavidus basilensis 4G11

Align Acetate/haloacid transporter, Dehp2, with a possible atypical topology (characterized)
to candidate RR42_RS03060 RR42_RS03060 MFS transporter

Query= TCDB::F8SVK1
         (552 letters)



>FitnessBrowser__Cup4G11:RR42_RS03060
          Length = 566

 Score =  774 bits (1998), Expect = 0.0
 Identities = 386/561 (68%), Positives = 458/561 (81%), Gaps = 10/561 (1%)

Query: 1   MATVSGQISHAPMTKEEKRVIFASSLGTVFEWYDFYLAGSLAAFISKSFFSGVNPTAAFI 60
           +A   G   ++ MT EE++VIFASSLGTVFEWYDFYL GSLAA I+K FFSG++PTAAFI
Sbjct: 7   VAIPGGNAQNSAMTAEERKVIFASSLGTVFEWYDFYLYGSLAAIIAKQFFSGLDPTAAFI 66

Query: 61  FTLLGFAAGFAVRPFGALVFGRLGDMVGRKYTFLITIVIMGLSTCVVGFLPGYAAIGMAS 120
           F LL FAAGF VRPFGALVFGRLGDM+GRKYTFL+TI+IMG ST +VG LPG+A+IG A+
Sbjct: 67  FALLAFAAGFIVRPFGALVFGRLGDMIGRKYTFLVTILIMGASTFIVGLLPGFASIGWAA 126

Query: 121 PVIFIAMRLLQGLALGGEYGGAATYVAEHAPANRRGFYTAWIQTTATLGLFLSLLVILGV 180
           P+I I +R+LQGLALGGEYGGAATYVAEHAP  +RG YTAWIQTTATLGLFLSL+VIL  
Sbjct: 127 PIILIGLRMLQGLALGGEYGGAATYVAEHAPHGKRGAYTAWIQTTATLGLFLSLIVILVC 186

Query: 181 RTAMGEDAFGAWGWRIPFVASLVLLGISVWIRMQLHESPAFERIKAEGKTSKAPLSEAFG 240
           R   G + F  WGWRIPF+ S++LLG+SV+IR+ + ESPAF+++KAEGKTSKAPL+EAFG
Sbjct: 187 RNMTGAN-FEVWGWRIPFLVSILLLGVSVYIRLSMSESPAFQKMKAEGKTSKAPLTEAFG 245

Query: 241 QWKNLKIVILALIGVTAGQAVVWYTGQFYALFFLTQTLKVDGASANILIAIALLIGTPFF 300
           QW+NLKIVILALIG+TAGQAVVWYTGQFY+LFFLTQ LKVD  +AN+LIA AL++GTPFF
Sbjct: 246 QWRNLKIVILALIGLTAGQAVVWYTGQFYSLFFLTQVLKVDATTANLLIAGALVVGTPFF 305

Query: 301 LFFGSLSDRIGRKPIILAGCLIAALTYFPLFKALTHYANPALEAATQKSPIVVIANPDEC 360
           +FFGSLSD++GRK II+AGC +A LTYFPLFKALTHYANPALE A Q + IVV A+P +C
Sbjct: 306 IFFGSLSDKVGRKWIIMAGCALAMLTYFPLFKALTHYANPALERAQQSAQIVVTADPKQC 365

Query: 361 SFQFNPVGTS-KFTSSCDIAKSALSKAGLNYDNVAAPAGTLAQIKVGDTTIDTYDGKAAD 419
           SFQ +P+     F SSCDI K  L++A  +Y+ V APAGT+A +K+GD  I +++     
Sbjct: 366 SFQGSPIAREIDFRSSCDIVKRTLAQASASYEVVEAPAGTVASVKIGDKEIASFNASLVP 425

Query: 420 A----KDAGK----AFDKNLGTALKAASYPPKADPSQLNWPMTVVILTILVIYVTMVYGP 471
           A     DA K    AF K +G ++ +A YP KADP+Q+N  M +V+L ILVIYVTMVYGP
Sbjct: 426 AGHSFDDASKKQIAAFKKQVGESMASAGYPTKADPAQMNTIMVLVVLVILVIYVTMVYGP 485

Query: 472 IAAMLVEMFPTRIRYTSMSLPYHIGNGWFGGFLPATAFAIVAAKGNIYSGLWYPIIIALA 531
           IAAMLVEMFPTRIRYTSMSLPYHIGNGWFGG LP  +FA+VA  GNIY GLWYPIIIA  
Sbjct: 486 IAAMLVEMFPTRIRYTSMSLPYHIGNGWFGGLLPTISFALVAQNGNIYYGLWYPIIIAGV 545

Query: 532 TFVIGLLFVRETKDSNIYAQD 552
           T V+G LF+RETKD +IYA D
Sbjct: 546 TLVLGSLFIRETKDVDIYAND 566


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: 890
Number of extensions: 36
Number of successful extensions: 8
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: 552
Length of database: 566
Length adjustment: 36
Effective length of query: 516
Effective length of database: 530
Effective search space:   273480
Effective search space used:   273480
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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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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