GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dctA in Azohydromonas australica DSM 1124

Align Organic acid uptake porter, DctA of 444 aas and 8 - 10 putative TMSs (characterized)
to candidate WP_051244599.1 H537_RS0138195 C4-dicarboxylate transporter DctA

Query= TCDB::Q848I3
         (444 letters)



>NCBI__GCF_000430725.1:WP_051244599.1
          Length = 454

 Score =  479 bits (1232), Expect = e-139
 Identities = 232/439 (52%), Positives = 326/439 (74%), Gaps = 5/439 (1%)

Query: 2   TTRQPLYKSLYFQVIVAIAIGILLGHFYPQTGVALKPLGDGFIKLIKMVIAPIIFCTVVS 61
           T R PL + LY QV++ I +G+ LGHFYP  G  +KPLGDGFIKLIKM++AP+IF T+V 
Sbjct: 9   TARVPLLRRLYVQVLIGILLGVALGHFYPAIGTDMKPLGDGFIKLIKMLLAPVIFATIVV 68

Query: 62  GIAGMQNMKSVGKTGGYALLYFEIVSTIALLIGLVVVNVVQPGNGMHIDVSTLDASKVAA 121
           GIA M ++K VGK G  ALLYFE++ST+AL++GL+VVNV++PG GM++D + LD   ++A
Sbjct: 69  GIARMGDLKEVGKVGAKALLYFEVLSTLALVVGLLVVNVIKPGVGMNVDPAALDGKSISA 128

Query: 122 YVTAGKDQ--SIVGFILNVIPNTIVGAFANGDILQVLMFSVIFGFALHRLGAYGKPVLDF 179
           Y +  + Q    V F++NVIP ++VG+FA G++LQ+L+F+V+FG A+ R G   +P +D 
Sbjct: 129 YTSMAESQHTGAVDFLMNVIPKSVVGSFAEGNVLQILLFAVLFGAAMSRFGDRVRPFIDM 188

Query: 180 IDRFAHVMFNIINMIMKLAPIGALGAMAFTIGAYGVGSLVQLGQLMICFYITCVLFVLVV 239
           +D F   MF I+ M+M LAPIGA GA+AFTIG YG+GS+   G+L++  Y TC LFVLVV
Sbjct: 189 LDMFLQGMFGIVRMVMVLAPIGAFGAIAFTIGKYGIGSMAAYGKLIVAVYATCALFVLVV 248

Query: 240 LGAICRAHGFSVLKLIRYIREELLIVLGTSSSESALPRMLIKMERLGAKKSVVGLVIPTG 299
           LGA+ R    S+   +RYIREELLI  GT+S+ES LP+M+ K+E  G +KS+VG+V+P G
Sbjct: 249 LGAVARICRISIRSYLRYIREELLITFGTASTESVLPQMMKKLEAAGCRKSIVGMVLPAG 308

Query: 300 YSFNLDGTSIYLTMAAVFIAQATDTHMDITHQITLLLVLLLSSKGAAGVTGSGFIVLAAT 359
           Y+FN DGT+IYLT+AAVF+AQAT+  + ++ Q+ +L VL+L+SKG+AGV G+GF+ LAAT
Sbjct: 309 YTFNPDGTAIYLTIAAVFVAQATNVPLSLSDQLVILSVLMLTSKGSAGVAGAGFVTLAAT 368

Query: 360 LSAVGHLPVAGLALILGIDRFMSEARALTNLVGNAVATVVVAKWVKELDEDQLQAELASG 419
           L ++  +PVAGL L+LG+DRF++EARA+TNL+GN +AT+ VAKW    DE +   E+  G
Sbjct: 369 LGSLHTIPVAGLVLLLGVDRFLNEARAITNLIGNGLATIAVAKWEGAFDEARWH-EVTGG 427

Query: 420 GRAISDTREEDDLGVAEGP 438
           G  ++  +  D L +   P
Sbjct: 428 G--VAQAQAGDGLPMESSP 444


Lambda     K      H
   0.326    0.142    0.402 

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: 641
Number of extensions: 21
Number of successful extensions: 2
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: 444
Length of database: 454
Length adjustment: 33
Effective length of query: 411
Effective length of database: 421
Effective search space:   173031
Effective search space used:   173031
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 (21.6 bits)
S2: 51 (24.3 bits)

This GapMind analysis is from Apr 09 2024. 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