GapMind for catabolism of small carbon sources

 

Aligments for a candidate for gcdG in Sinorhizobium meliloti 1021

Align succinyl-CoA-glutarate CoA-transferase (EC 2.8.3.13) (characterized)
to candidate SM_b21182 SM_b21182 hypothetical protein

Query= reanno::pseudo5_N2C3_1:AO356_10845
         (406 letters)



>lcl|FitnessBrowser__Smeli:SM_b21182 SM_b21182 hypothetical protein
          Length = 394

 Score =  421 bits (1083), Expect = e-122
 Identities = 217/388 (55%), Positives = 266/388 (68%), Gaps = 8/388 (2%)

Query: 4   LSHLRVLDLSRVLAGPWAGQILADLGADVIKVERPGNGDDTRAWGPPFLKDARGENTTEA 63
           L  +RVL+L+R+LAGPW GQ LADLGADVIKVE P  GDDTR WGPPF+     E   +A
Sbjct: 5   LKGIRVLELARILAGPWIGQTLADLGADVIKVESPA-GDDTRTWGPPFVTGEDDERL-DA 62

Query: 64  AYYLSANRNKQSVTIDFTRPEGQRLVRELAAKSDILIENFKVGGLAAYGLDYDSLKAINP 123
           AY+ + NR K+SV +DFT  EGQ  VR LAA+SD+L+ENFKVGGLA YGLDY+SL  +NP
Sbjct: 63  AYFHACNRGKRSVVLDFTTAEGQEAVRRLAAQSDVLLENFKVGGLAKYGLDYESLSKVNP 122

Query: 124 QLIYCSITGFGQTGPYAKRAGYDFMIQGLGGLMSLTGRPEGDEGAGPVKVGVALTDILTG 183
           +LIYCS+TGFGQ GPYA RAGYD+++QG+ G+M LTG P+ +    P K+GVA  DI TG
Sbjct: 123 RLIYCSVTGFGQDGPYAHRAGYDYIVQGMSGIMDLTGEPDRE----PQKIGVAFADIFTG 178

Query: 184 LYSTAAILAALAHRDHVGGGQHIDMALLDVQVACLANQAMNYLTTGNAPKRLGNAHPNIV 243
           LY   A+ AALA R+  G GQ IDMALLD     LANQA+N+L +G AP+RLGNAHPNI 
Sbjct: 179 LYGVIAVQAALAQRERTGEGQQIDMALLDCMTGVLANQALNFLVSGKAPRRLGNAHPNIA 238

Query: 244 PYQDFPTADGDFILTVGNDGQFRKFAEVAGQPQWADDPRFATNKVRVANRAVLIPLIRQA 303
           PYQ FPT+DG  I+ VGND QF KF E+ G+P  A D R+ TN  RV +R  L P +   
Sbjct: 239 PYQVFPTSDGHLIVAVGNDRQFVKFCELLGRPDLAADARYRTNADRVQHRDSLTPELAAE 298

Query: 304 TVFKTTAEWVTQLEQAGVPCGPINDLAQVFADPQVQARGLAMELPH--LLAGKVPQVASP 361
           T        + +LE +GVP GPIN +A VFADPQ+  R + ++ PH    AG  P V +P
Sbjct: 299 TAKYERDTLLEKLEASGVPGGPINTVADVFADPQIVHRQMRVDTPHTGAAAGTSPGVRTP 358

Query: 362 IRLSETPVEYRNAPPLLGEHTLEVLQRV 389
           IR S   +      P LGEHT EVL  +
Sbjct: 359 IRFSGATLALDRGVPRLGEHTAEVLAEI 386


Lambda     K      H
   0.319    0.137    0.408 

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: 496
Number of extensions: 21
Number of successful extensions: 5
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: 394
Length adjustment: 31
Effective length of query: 375
Effective length of database: 363
Effective search space:   136125
Effective search space used:   136125
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 (21.7 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 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, the preprint on GapMind for carbon sources, 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