GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lacF in Synechococcus elongatus PCC 7942

Align ABC transporter for Lactose, permease component 1 (characterized)
to candidate Synpcc7942_0526 Synpcc7942_0526 ABC-type sugar transport systems permease components-like

Query= reanno::Smeli:SM_b21653
         (298 letters)



>FitnessBrowser__SynE:Synpcc7942_0526
          Length = 293

 Score =  171 bits (433), Expect = 2e-47
 Identities = 97/277 (35%), Positives = 155/277 (55%), Gaps = 8/277 (2%)

Query: 17  WLFVAPALGLITLFMVYPIAWSLWMSFQS---GRGMTLKFAGFANIVRLWNDPVFIKALT 73
           +LF+APAL ++ L + +P   + + SF         + ++ G  N  RL ND VF K L 
Sbjct: 11  YLFLAPALTILGLTVFWPALQAFYFSFTRFDYNLTRSPQWVGLENFQRLLNDAVFWKTLG 70

Query: 74  NTMTYFVVQVPIMILLALILASLLNNPRLVGRGVFRTAIFLPCVSSLVAYSVLFKGMFAT 133
           NT  Y +  VP+++ L L LA L+N P L G  +FR A + P + S+V   + ++ ++A 
Sbjct: 71  NTFIYLIGVVPLLVFLPLGLAILVNRP-LRGITLFRLAYYTPVIVSIVVAGIAWRWLYAE 129

Query: 134 DGIVNSTLQAI-GLAASPIPWLTHPFWAKVLVILAITWRWTGYNMIFYLAALQNIDKSIY 192
            G++N   Q + G    PIPWLT P  A   V+    W+  GY M+ YLA LQ I   +Y
Sbjct: 130 TGLLNQLGQLVFGEGFQPIPWLTSPALALFSVMAVTVWKGLGYYMVIYLAGLQGIPLELY 189

Query: 193 EVARIDGVPAWARLTHLTIPLLKPVILFTTVISTIGTLQLFDEVYNLTEGKGGPSNATLT 252
           E A +DG   W R   +T+PL++P ++   VIS I   ++F+EV+ +T+  GGP N++ T
Sbjct: 190 EAAALDGSDGWRRHLDITLPLMRPYLVLVAVISAISATKVFEEVFIMTQ--GGPLNSSKT 247

Query: 253 LSLYIYNLTFRFMPNLGYAATVSYVIVVLVALLAFVQ 289
           +  Y+Y   F+ +  + YA TV   + ++V  L+ ++
Sbjct: 248 VVYYVYQQAFQKL-EVSYACTVGLALFLVVLTLSLLR 283


Lambda     K      H
   0.330    0.142    0.447 

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: 280
Number of extensions: 16
Number of successful extensions: 4
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: 298
Length of database: 293
Length adjustment: 26
Effective length of query: 272
Effective length of database: 267
Effective search space:    72624
Effective search space used:    72624
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 (21.9 bits)
S2: 48 (23.1 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