GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dctA in Mesorhizobium ciceri WSM1271

Align C4-dicarboxylate transporter (substrates: fumarate, D- and L-malate, succinate, succinamide, orotate, iticonate, mesaconate) (characterized)
to candidate YP_004144924.1 Mesci_5852 sodium:dicarboxylate symporter

Query= TCDB::Q01857
         (444 letters)



>NCBI__GCF_000185905.1:YP_004144924.1
          Length = 452

 Score =  635 bits (1638), Expect = 0.0
 Identities = 325/433 (75%), Positives = 372/433 (85%)

Query: 2   IAAPLDAVAGSKGKKPFYSHLYVQVLVAIAAGILLGHFYPELGTQLKPLGDAFIKLVKMI 61
           + AP    AG   +K FY+ LYVQVL AIA G+ +G+ YP  G  LKPLGDAFIKLVKMI
Sbjct: 20  LLAPPIRSAGPPARKAFYAQLYVQVLTAIALGVAVGYLYPGTGEALKPLGDAFIKLVKMI 79

Query: 62  IAPVIFLTVATGIAGMSDLQKVGRVAGKAMLYFLTFSTLALIIGLIVANVVQPGAGMNID 121
           IAPVIFLTV TGIAGM+DL+KVGRVAGKAM+YFLTFS+LAL++GL+VANVVQPG+G++ID
Sbjct: 80  IAPVIFLTVTTGIAGMNDLKKVGRVAGKAMIYFLTFSSLALMVGLVVANVVQPGSGLDID 139

Query: 122 PASLDPAAVATFAAKAHEQSIVGFLTNIIPTTIVGAFADGDILQVLFFSVLFGIALAMVG 181
           PASLD  AV  + AK H+QS+ GFL NIIP+TIVGAFA+G+ILQVLFFS+LFG ALAM G
Sbjct: 140 PASLDGQAVQGYVAKVHDQSVTGFLMNIIPSTIVGAFAEGNILQVLFFSILFGSALAMAG 199

Query: 182 EKGEQVVNFLNSLTAPVFKLVAILMKAAPIGAFGAMAFTIGKYGVGSIANLAMLIGTFYI 241
           + G+ V++ L +L APVFKLV ILM+AAP+GAFGAMAFTIGKYG+GS+ NLAML+ TFY 
Sbjct: 200 DTGKPVLSLLQALLAPVFKLVGILMQAAPVGAFGAMAFTIGKYGIGSVVNLAMLVATFYF 259

Query: 242 TSLLFVFIVLGAVARYNGFSIVALLRYIKEELLLVLGTSSSEAALPGLMNKMEKAGCKRS 301
           T+ +FVF +LGAV RYNGFSI +L+RYIKEELLLVL TSSSEAALP LM KMEKAG KRS
Sbjct: 260 TAFVFVFGILGAVCRYNGFSIFSLVRYIKEELLLVLATSSSEAALPSLMEKMEKAGAKRS 319

Query: 302 VVGLVIPTGYSFNLDGTNIYMTLAALFIAQATGIHLSWGDQILLLLVAMLSSKGAAGITG 361
           VVGLVIPTGYSFNLDGTNIYMTLAALFIAQAT  HLS  DQILLL+VAMLSSKGAAGITG
Sbjct: 320 VVGLVIPTGYSFNLDGTNIYMTLAALFIAQATNTHLSVADQILLLVVAMLSSKGAAGITG 379

Query: 362 AGFITLAATLSVVPSVPVAGMALILGIDRFMSECRALTNLVGNAVATIVVARWENELDTV 421
           AGF+TLAATLSV+P+VPVAGMALILG+DRFMSECRALTN+VGNAVA +VVARWE ELD  
Sbjct: 380 AGFVTLAATLSVIPTVPVAGMALILGVDRFMSECRALTNVVGNAVAALVVARWEGELDEA 439

Query: 422 QLAAALGGQTGED 434
           ++ AA  G    D
Sbjct: 440 RMKAAFCGSLPRD 452


Lambda     K      H
   0.324    0.139    0.393 

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: 727
Number of extensions: 20
Number of successful extensions: 1
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: 452
Length adjustment: 33
Effective length of query: 411
Effective length of database: 419
Effective search space:   172209
Effective search space used:   172209
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: 51 (24.3 bits)

This GapMind analysis is from Sep 24 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