GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__SynE:Synpcc7942_2132 Synpcc7942_2132
           phosphoglucosamine mutase
          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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

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