GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lacC in Magnetospirillum magneticum AMB-1

Align 6-phosphofructokinase isozyme 1; EC 2.7.1.11 (characterized)
to candidate WP_011384698.1 AMB_RS11635 ATP-dependent 6-phosphofructokinase

Query= CharProtDB::CH_024070
         (320 letters)



>NCBI__GCF_000009985.1:WP_011384698.1
          Length = 361

 Score =  216 bits (551), Expect = 5e-61
 Identities = 135/331 (40%), Positives = 185/331 (55%), Gaps = 35/331 (10%)

Query: 3   KKIGVLTSGGDAPGMNAAIRGVVRSALTE-GLEVMGIYDGYLGLYEDRM--VQLDRYSVS 59
           K+IG+LTSGGD  G+NAA+R VV  A+   G +V GI DG LGL    +  V+ D  SV 
Sbjct: 4   KRIGILTSGGDCAGLNAALRAVVHRAIRNYGWKVFGIRDGSLGLMNRPLNYVEFDLKSVG 63

Query: 60  D-MINRGGTFLGSAR--------FPEFRDENIRAVAIENLKKRGIDALVVIGGDGSYMGA 110
           D M+  GGT LG+           P+   ++     ++  K+ GI+ALVVIGGDGS    
Sbjct: 64  DDMLRLGGTILGTINKGDPFAYPMPDGSKKDRSQDFVDGYKELGIEALVVIGGDGSMRIL 123

Query: 111 MRLTEMG-FPCIGLPGTIDNDIKGTDYTIGFFTALSTVVEAIDRLRDTSSSHQRISVVEV 169
             L   G  P +G+P TIDND+  TDY IGF TAL+   EA+DRL  T++SH R+ ++EV
Sbjct: 124 NELCRKGGIPMVGIPKTIDNDVAQTDYAIGFATALNVAGEAMDRLAPTAASHHRVMILEV 183

Query: 170 MGRYCGDLTLAAAIAGGCEFVVVPEVEFSREDLVNEIKAGIAKGKKHAIVAITEHMCDVD 229
           MGR  G + L A IAGG + V++PE+ ++ E +  +I     +G+ HA++ + E  C  +
Sbjct: 184 MGRDVGHIALNAGIAGGADVVLIPEIPYTLEGIAKKIAEVRDEGRNHALMVVAEG-CKTE 242

Query: 230 E---------------------LAHFIEKETGRETRATVLGHIQRGGSPVPYDRILASRM 268
                                 LA  + +    ETR TVLGH+QRGG P   DRI+AS  
Sbjct: 243 TGESVTTLQSGGQARYGGIGQYLAARLAETVEAETRVTVLGHVQRGGMPAMRDRIIASAF 302

Query: 269 GAYAIDLLLAGYGGRCVGIQNEQLVHHDIID 299
           G YA+DL+  G  GR V  Q+ Q+V   I D
Sbjct: 303 GVYAVDLIAQGKLGRMVAWQHGQVVDVPITD 333


Lambda     K      H
   0.322    0.141    0.413 

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: 358
Number of extensions: 14
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: 320
Length of database: 361
Length adjustment: 28
Effective length of query: 292
Effective length of database: 333
Effective search space:    97236
Effective search space used:    97236
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 (21.9 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