GapMind for catabolism of small carbon sources

 

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

Align succinyl-CoA-glutarate CoA-transferase (EC 2.8.3.13) (characterized)
to candidate WP_011383897.1 AMB_RS07510 CoA transferase

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



>NCBI__GCF_000009985.1:WP_011383897.1
          Length = 401

 Score =  532 bits (1370), Expect = e-156
 Identities = 262/405 (64%), Positives = 315/405 (77%), Gaps = 6/405 (1%)

Query: 2   GALSHLRVLDLSRVLAGPWAGQILADLGADVIKVERPGNGDDTRAWGPPFLKDARGENTT 61
           GALSHLR+LDLSRVLAGPWAGQ+LAD+GA+V+K+E+PG GDDTRAWGPPFL    G    
Sbjct: 3   GALSHLRILDLSRVLAGPWAGQLLADMGAEVLKIEKPGEGDDTRAWGPPFLDADEGRG-- 60

Query: 62  EAAYYLSANRNKQSVTIDFTRPEGQRLVRELAAKSDILIENFKVGGLAAYGLDYDSLKAI 121
           E+AYYLSANR K SVTIDFT+P+GQ LVR L A+ D+++ENFKVGGLA YGLDYDSLKAI
Sbjct: 61  ESAYYLSANRGKHSVTIDFTQPQGQALVRRLVAQCDVVLENFKVGGLAKYGLDYDSLKAI 120

Query: 122 NPQLIYCSITGFGQTGPYAKRAGYDFMIQGLGGLMSLTGRPEGDEGAGPVKVGVALTDIL 181
            P L+YCSITGFGQ GPYA+RAGYDF++QG+GGLMSLTG P+G+    P+KVGVALTDI 
Sbjct: 121 KPDLVYCSITGFGQDGPYAQRAGYDFLVQGMGGLMSLTGTPDGE----PMKVGVALTDIF 176

Query: 182 TGLYSTAAILAALAHRDHVGGGQHIDMALLDVQVACLANQAMNYLTTGNAPKRLGNAHPN 241
           TG+Y+  A+LAALAHRD  G GQHID+ALLDVQVA LANQA NYL  G  PKRLGN+HPN
Sbjct: 177 TGMYAGFAVLAALAHRDRTGEGQHIDLALLDVQVAVLANQATNYLVGGVIPKRLGNSHPN 236

Query: 242 IVPYQDFPTADGDFILTVGNDGQFRKFAEVAGQPQWADDPRFATNKVRVANRAVLIPLIR 301
           IVPYQ F TA+G  IL +GND QFR+F EVAG P+   DP +ATN  RV +RA+L+P++ 
Sbjct: 237 IVPYQAFATAEGHIILAIGNDAQFRRFCEVAGHPELGTDPLYATNADRVRHRAILVPVLV 296

Query: 302 QATVFKTTAEWVTQLEQAGVPCGPINDLAQVFADPQVQARGLAMELPHLLAGKVPQVASP 361
           +         W+ +LE+AGVPCGPIN L +VFADPQV+ RG+A+ + H     +  VA+P
Sbjct: 297 EIMTEHDADYWIAELEKAGVPCGPINSLDRVFADPQVKHRGMAVAMEHPQREDLRLVANP 356

Query: 362 IRLSETPVEYRNAPPLLGEHTLEVLQRVLGLDEAAVMAFREAGVL 406
           I LS+TPV Y   PPLLG  T +VL R+LGLDE      R +GV+
Sbjct: 357 IHLSKTPVTYDRPPPLLGADTDDVLARLLGLDEGERAELRSSGVI 401


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: 614
Number of extensions: 22
Number of successful extensions: 3
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: 401
Length adjustment: 31
Effective length of query: 375
Effective length of database: 370
Effective search space:   138750
Effective search space used:   138750
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 (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