GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dctA in Klebsiella michiganensis M5al

Align aerobic C4-dicarboxylate transport protein (characterized)
to candidate BWI76_RS26760 BWI76_RS26760 C4-dicarboxylate transporter DctA

Query= CharProtDB::CH_014038
         (428 letters)



>FitnessBrowser__Koxy:BWI76_RS26760
          Length = 428

 Score =  771 bits (1992), Expect = 0.0
 Identities = 402/428 (93%), Positives = 416/428 (97%)

Query: 1   MKTSLFKSLYFQVLTAIAIGILLGHFYPEIGEQMKPLGDGFVKLIKMIIAPVIFCTVVTG 60
           MK S FKSLY QVL+AIAIGILLGHFYPE+G QMKPLGD FVKLIKMIIAPVIFCTVVTG
Sbjct: 1   MKISFFKSLYVQVLSAIAIGILLGHFYPELGAQMKPLGDAFVKLIKMIIAPVIFCTVVTG 60

Query: 61  IAGMESMKAVGRTGAVALLYFEIVSTIALIIGLIIVNVVQPGAGMNVDPATLDAKAVAVY 120
           IAGMESMKAVGRTGAVALLYFEIVSTIALIIGLIIVNVVQPGAGMNVDPATLDAKAVAVY
Sbjct: 61  IAGMESMKAVGRTGAVALLYFEIVSTIALIIGLIIVNVVQPGAGMNVDPATLDAKAVAVY 120

Query: 121 ADQAKDQGIVAFIMDVIPASVIGAFASGNILQVLLFAVLFGFALHRLGSKGQLIFNVIES 180
           A+QAKDQGIVAF++D+IP SVIGAFASGNILQVL+FAVLFGFALHRLGSKGQLIFNVIES
Sbjct: 121 AEQAKDQGIVAFLLDIIPGSVIGAFASGNILQVLMFAVLFGFALHRLGSKGQLIFNVIES 180

Query: 181 FSQVIFGIINMIMRLAPIGAFGAMAFTIGKYGVGTLVQLGQLIICFYITCILFVVLVLGS 240
           FSQVIFGIINMIMRLAPIGAFGAMAFTIGKYGVGTLVQLGQLI+CFYITCILFVV+VLGS
Sbjct: 181 FSQVIFGIINMIMRLAPIGAFGAMAFTIGKYGVGTLVQLGQLIVCFYITCILFVVVVLGS 240

Query: 241 IAKATGFSIFKFIRYIREELLIVLGTSSSESALPRMLDKMEKLGCRKSVVGLVIPTGYSF 300
           IAKATGFSIFKFIRYIREELLIVLGTSSSESALPRMLDKMEKLGCRKSVVGLVIPTGYSF
Sbjct: 241 IAKATGFSIFKFIRYIREELLIVLGTSSSESALPRMLDKMEKLGCRKSVVGLVIPTGYSF 300

Query: 301 NLDGTSIYLTMAAVFIAQATNSQMDIVHQITLLIVLLLSSKGAAGVTGSGFIVLAATLSA 360
           NLDGTSIYLTMAAVFIAQATNS MDI HQITLL+VLLLSSKGAAGVTGSGFIVLAAT+SA
Sbjct: 301 NLDGTSIYLTMAAVFIAQATNSHMDIFHQITLLVVLLLSSKGAAGVTGSGFIVLAATISA 360

Query: 361 VGHLPVAGLALILGIDRFMSEARALTNLVGNGVATIVVAKWVKELDHKKLDDVLNNRAPD 420
           VGHLPVAGLALILGIDRFMSEARALTNLVGNGVATIVVAKWVKELD ++LDDVLNNR P 
Sbjct: 361 VGHLPVAGLALILGIDRFMSEARALTNLVGNGVATIVVAKWVKELDSQQLDDVLNNRTPV 420

Query: 421 GKTHELSS 428
            K+HELSS
Sbjct: 421 NKSHELSS 428


Lambda     K      H
   0.327    0.142    0.401 

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: 765
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: 428
Length of database: 428
Length adjustment: 32
Effective length of query: 396
Effective length of database: 396
Effective search space:   156816
Effective search space used:   156816
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 (21.7 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