GapMind for catabolism of small carbon sources

 

Alignments for a candidate for andAa in Sinorhizobium meliloti 1021

Align Anthranilate 1,2-dioxygenase system ferredoxin--NAD(+) reductase component; EC 1.18.1.3 (characterized)
to candidate SMc01990 SMc01990 ferredoxin reductase

Query= SwissProt::Q84BZ0
         (406 letters)



>FitnessBrowser__Smeli:SMc01990
          Length = 409

 Score =  246 bits (627), Expect = 1e-69
 Identities = 152/411 (36%), Positives = 221/411 (53%), Gaps = 12/411 (2%)

Query: 1   MSADPFVIVGAGHAARRTAEALRARDADAPIVMIGAERELPYDRPALSKDALLNDDGEQR 60
           M  +  VIVG G A  R A+ L    A+  I +IG E   PY+RP LSK  LL     + 
Sbjct: 1   MMPERIVIVGGGQAGGRVAQILAGSPANLDIALIGLEPHPPYNRPPLSKGVLLGKSELKD 60

Query: 61  AFVRDAAWYDAQRIALRLGTRVDAIEREAQRVRLDDGTTLPYAKLVLATGSRVRTFGGPI 120
             +       A R+    G R ++++  A+ V  DDG  L Y KLVLATGSRVR    P 
Sbjct: 61  CVIWPQGDATAGRVRFYPGRRAESLDIHARHVITDDGARLDYDKLVLATGSRVRRLSVPG 120

Query: 121 DAGVVAHYVRTVADARALRAQLVRGRRVAVLGGGFIGLEVAAAARQLGCNVTVIDPAARL 180
                   +RT  DA A+  +  R +R+ V+GGGF+GLE+AAAAR  G    V++   RL
Sbjct: 121 AECDGVFTLRTFDDAVAIARRFHRSKRLLVVGGGFVGLEIAAAARSRGLETVVVEATNRL 180

Query: 181 LQRALPEVVGAYAHRLHDERGVGFQMATLPRAIRAAAGGG--AIVETDRGDVHADVVVVG 238
           L R +P+ +GA   R H+  GV F++ ++   + A   G   + V ++   V  D+ V+G
Sbjct: 181 LSRIVPQEIGAALARYHEAAGVSFRVGSMVEKLVANRSGKLKSAVLSNGETVPCDLAVIG 240

Query: 239 IGVLPNVELAQAAGLDVDNGIRVDAGCRTADRAIFAAGEVTMHFNPLLGRHVRIESWQVA 298
           +GV  N ELA+ AGL+V  GIR D+  R +   ++A G+    ++PL  R+VR+E+WQ A
Sbjct: 241 VGVTANTELAKEAGLEVQVGIRTDSALRASADGVYACGDAVSFWHPLFERYVRVEAWQNA 300

Query: 299 ENQPAVAAANLLGADDAYAELPWLWSDQYDCNLQMLGL--FGAGQTTVVRGDPARGPFTV 356
           E+   V A+ LLG D     +P+ WSDQY+ ++Q+ G+  FG+   T    +       +
Sbjct: 301 EDHARVVASQLLGQDMVCDTVPFFWSDQYEWSMQIAGIPYFGSQLVT----NTVEEAKIL 356

Query: 357 FGLGGDGRIVAAAAVN----LGRDIGAARRLIAAGAMPDPQQLADPTVGLK 403
           + L   GR+VAA  +     +GR I  ARRLI   A P+PQ L    + L+
Sbjct: 357 YHLDARGRLVAATGLGHDRLIGRKIAEARRLIKRRARPNPQMLKTGQIQLE 407


Lambda     K      H
   0.322    0.138    0.410 

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: 362
Number of extensions: 19
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: 406
Length of database: 409
Length adjustment: 31
Effective length of query: 375
Effective length of database: 378
Effective search space:   141750
Effective search space used:   141750
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: 50 (23.9 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