GapMind for catabolism of small carbon sources

 

Alignments for a candidate for deoB in Synechococcus elongatus PCC 7942

Align phosphopentomutase (EC 5.4.2.7) (characterized)
to candidate Synpcc7942_2132 Synpcc7942_2132 phosphoglucosamine mutase

Query= BRENDA::Q6I7B6
         (450 letters)



>FitnessBrowser__SynE:Synpcc7942_2132
          Length = 472

 Score =  158 bits (399), Expect = 4e-43
 Identities = 135/446 (30%), Positives = 215/446 (48%), Gaps = 46/446 (10%)

Query: 3   LFGTAGIRGTLWEKVTPELAMKVGMAVGTY------KSGKALVGRDGRTSSVMLKNAMIS 56
           LFGT GIRG + E +T  LA +VG   G          G  +VG+D R SS ML  A+ S
Sbjct: 26  LFGTDGIRGRVGEHLTAPLAQQVGFWTGQVLRQAGGDRGPVVVGQDSRNSSNMLAMALSS 85

Query: 57  GLLSTGMEVLDADLIPTPALAWGT-RKLADAGVMITASHNPPTDNGVKVFNGDGTEFYVE 115
           GL + G+EVL   L PTP +A+ T    A  GVMI+ASHNPP DNG+KVF  DG++    
Sbjct: 86  GLAAAGVEVLHLGLCPTPGVAYLTHHSEAIGGVMISASHNPPGDNGIKVFGADGSKL--- 142

Query: 116 QERGLEEIIFSG------NFRKARWDEIKPVRNVEVIPDYINAVLDFVGHETN---LKVL 166
            +R L+  I +G      +     W +       ++   Y  A+   +G   N   LK++
Sbjct: 143 -DRQLQAAIEAGLRGQQTSLPATTWGQ--HYYQPQLADHYQAAIAQSLGQRANLQGLKIV 199

Query: 167 YDGANGAGSLVAPYLLREMGAKVLSVNAHVDGHFPGRKPEPRYENIAYLGKLVRELGVDL 226
            D A GA +L+AP L RE+GA+V++++   DG+           ++A L   V E G D+
Sbjct: 200 LDLAWGAAALLAPRLFRELGAEVIALHDLPDGN--QINVNCGSTHLARLQAAVLEQGADM 257

Query: 227 AIAQDGDADRIAVFDEKGNYVDEDTVIALFAKLYVEEH--GGGTVVVSIDTGSRIDAVVE 284
             A DGDADR+   D +G  VD D ++ L+ +   ++    G  +V ++      +   +
Sbjct: 258 GFAFDGDADRVLAVDGRGRSVDGDHILFLWGRELEQQQQLPGQAIVTTVMANLGFERAWQ 317

Query: 285 RAGGRVVRIPLGQPH---DGIKRYKAIFAAEPWKLVHPKFGPWIDPFVTMGLLIKLIDEN 341
             GG  VR  +G  +   +   R   +   +   ++   +    D  +T   +  L+  +
Sbjct: 318 AVGGEFVRTAVGDQYVQAEMQARGAMLGGEQSGHILCRHYALTGDGTLTAAHVAALVQAS 377

Query: 342 G-PLSELVKEIPTYYLKKANVLCPDEYKAEVVRRA-AEEVERKLSSEIKEVLT--ISGFR 397
           G  L++LV +    Y              +++R    E+ +R+ + +    LT  I+   
Sbjct: 378 GVSLADLVDQSFRPY-------------PQLLRNVRVEDRDRRCNWQNCAALTQAIAAAE 424

Query: 398 IALNDGSWILIRPSGTEPKIRVVAEA 423
             + D   +L+R SGTEP +R++ EA
Sbjct: 425 TDMGDRGRVLVRASGTEPLLRIMVEA 450


Lambda     K      H
   0.318    0.138    0.402 

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: 474
Number of extensions: 21
Number of successful extensions: 6
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 450
Length of database: 472
Length adjustment: 33
Effective length of query: 417
Effective length of database: 439
Effective search space:   183063
Effective search space used:   183063
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 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