GapMind for catabolism of small carbon sources

 

Alignments for a candidate for malK in Synechococcus elongatus PCC 7942

Align ABC-type maltose transporter (subunit 3/3) (EC 7.5.2.1) (characterized)
to candidate Synpcc7942_0947 Synpcc7942_0947 ATPase

Query= BRENDA::P68187
         (371 letters)



>FitnessBrowser__SynE:Synpcc7942_0947
          Length = 355

 Score =  270 bits (689), Expect = 6e-77
 Identities = 148/358 (41%), Positives = 221/358 (61%), Gaps = 20/358 (5%)

Query: 3   SVQLQNVTKAWGEVVVS-KDINLDIHEGEFVVFVGPSGCGKSTLLRMIAGLETITSGDLF 61
           +++L+ + KA+   VV   +++L +  GEF+  +GPSGCGKST LR+IAGL+  TSG ++
Sbjct: 5   ALELRQLRKAYSPSVVPVANLSLQLQPGEFLTLLGPSGCGKSTTLRLIAGLDQPTSGSIW 64

Query: 62  IGEKRMNDTPPAERGVGMVFQSYALYPHLSVAENMSFGLKLAGAKKEVINQRVNQVAEVL 121
           +G++ +   PP +R + MVFQSYALYPHL+V +N++ GL++       I QR+ QVA  L
Sbjct: 65  LGDREITTLPPGDRDMAMVFQSYALYPHLNVRQNLTLGLQIRRTSAAEIEQRLQQVAHNL 124

Query: 122 QLAHLLDRKPKALSGGQRQRVAIGRTLVAEPSVFLLDEPLSNLDAALRVQMRIEISRLHK 181
           +L HLLDR+P  LSGGQRQRVA+GR LV +PSVFLLDEPLSNLDA LR Q+R ++  L  
Sbjct: 125 ELDHLLDRRPAQLSGGQRQRVALGRALVRQPSVFLLDEPLSNLDALLREQVRAQMKALFS 184

Query: 182 RLGRTMIYVTHDQVEAMTLADKIVVLDAGRVAQVGKPLELYHYPADRFVAGFIGSPKMNF 241
           +    ++YVTHDQ EA++L+ +I +L+ G + Q+  P  +Y  PA+ FVAGFIGSP+MN 
Sbjct: 185 QQASPVVYVTHDQTEALSLSHRIAILNGGHLQQLDSPDRIYQAPANAFVAGFIGSPRMNL 244

Query: 242 LPVKVTATAIDQVQVELPMPNRQQVWLPVESRDVQVGANMSLGIRPEHL-LPSDIADVIL 300
           LP+ + +         LP+P+            +   + +  G+RPEHL L +   +  +
Sbjct: 245 LPLPIHSGQAWLGSRALPIPSH-----------LAARSQVLWGLRPEHLKLATPEVERAI 293

Query: 301 EGEVQVVEQLGNETQIHIQI---PSIRQNLVYRQNDVVLVEEGATFAIGLPPERCHLF 355
             ++ + E LG +  + + I   P +R  L+   +  +  +   TF     PE  H F
Sbjct: 294 PVQLHLTENLGMQRLLTVAIAANPEVRLRLLMPSDQPIPTDLQVTF----EPESQHWF 347


Lambda     K      H
   0.320    0.137    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: 377
Number of extensions: 13
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: 371
Length of database: 355
Length adjustment: 29
Effective length of query: 342
Effective length of database: 326
Effective search space:   111492
Effective search space used:   111492
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 49 (23.5 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