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_011383259.1 AMB_RS08365 CoA transferase

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



>NCBI__GCF_000009985.1:WP_011383259.1
          Length = 403

 Score =  536 bits (1381), Expect = e-157
 Identities = 272/405 (67%), Positives = 309/405 (76%), Gaps = 4/405 (0%)

Query: 2   GALSHLRVLDLSRVLAGPWAGQILADLGADVIKVERPGNGDDTRAWGPPFLKDARGENTT 61
           G LSHLRVLDLSRVLAGPWAGQ+LAD+GA+VIKVERPG GDDTR WGPPFLKD +G +T 
Sbjct: 3   GPLSHLRVLDLSRVLAGPWAGQLLADMGAEVIKVERPGEGDDTRGWGPPFLKDGQGGDTG 62

Query: 62  EAAYYLSANRNKQSVTIDFTRPEGQRLVRELAAKSDILIENFKVGGLAAYGLDYDSLKAI 121
           EAAY+LSANR K+SVTIDFT+ +GQ LVR LAA+SD+++ENFKVGGLA YGLDY SLKA+
Sbjct: 63  EAAYFLSANRGKRSVTIDFTQAQGQELVRRLAARSDVVLENFKVGGLAKYGLDYASLKAV 122

Query: 122 NPQLIYCSITGFGQTGPYAKRAGYDFMIQGLGGLMSLTGRPEGDEGAGPVKVGVALTDIL 181
            P L+YCSITGFGQ GPYA+RAGYDF+IQG+GGLMSLTG P G     P+KVGVALTDI 
Sbjct: 123 KPDLVYCSITGFGQDGPYAQRAGYDFLIQGMGGLMSLTGEPGGQ----PMKVGVALTDIF 178

Query: 182 TGLYSTAAILAALAHRDHVGGGQHIDMALLDVQVACLANQAMNYLTTGNAPKRLGNAHPN 241
           TG+Y+  AILAALA RD  G G  ID+ALLDVQVA LANQA NYL  G  PKRLGNAHPN
Sbjct: 179 TGMYAGFAILAALAKRDRTGEGSQIDLALLDVQVAVLANQATNYLVGGATPKRLGNAHPN 238

Query: 242 IVPYQDFPTADGDFILTVGNDGQFRKFAEVAGQPQWADDPRFATNKVRVANRAVLIPLIR 301
           IVPYQ F TADG  IL VGNDGQFR+F   AG+P+   DPRFATN  RV NRA L+PL+ 
Sbjct: 239 IVPYQAFATADGHIILAVGNDGQFRRFCHTAGRPELGADPRFATNVERVRNRAELVPLLE 298

Query: 302 QATVFKTTAEWVTQLEQAGVPCGPINDLAQVFADPQVQARGLAMELPHLLAGKVPQVASP 361
                + +A W+ +LE+AGVPCGPINDLA VFADPQV  RGL   L H LAG +  VA+P
Sbjct: 299 ALLTSRPSARWIAELEEAGVPCGPINDLANVFADPQVIHRGLRTRLDHPLAGGIDLVANP 358

Query: 362 IRLSETPVEYRNAPPLLGEHTLEVLQRVLGLDEAAVMAFREAGVL 406
           IR          APPLLG  T EVL   LG+    +   RE GV+
Sbjct: 359 IRFDGAQALSDRAPPLLGADTAEVLGGWLGMGADEMERLRENGVV 403


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: 649
Number of extensions: 27
Number of successful extensions: 2
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: 403
Length adjustment: 31
Effective length of query: 375
Effective length of database: 372
Effective search space:   139500
Effective search space used:   139500
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.

Links

Downloads

Related tools

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