GapMind for catabolism of small carbon sources

 

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

Align succinate-semialdehyde dehydrogenase (EC 1.2.1.16) (characterized)
to candidate WP_011384974.1 AMB_RS13050 aldehyde dehydrogenase family protein

Query= reanno::pseudo3_N2E3:AO353_11505
         (480 letters)



>NCBI__GCF_000009985.1:WP_011384974.1
          Length = 479

 Score =  300 bits (769), Expect = 5e-86
 Identities = 181/478 (37%), Positives = 262/478 (54%), Gaps = 28/478 (5%)

Query: 14  FIDGAWVDADNG-QTINVTNPATGEILGTVPKMGAAETRRAIEAADKALPAWRALTAKER 72
           ++DGAWV    G + ++V NPAT ++ G V   GA +  RAI+AA KA PAW A    ER
Sbjct: 8   YVDGAWVKPAKGSRLLDVINPATEQVSGRVALGGADDAVRAIQAAAKAFPAWAATPLAER 67

Query: 73  ANKLRRWFELIIENQDDLARLMTLEQGKPL------AEAK---GEIVYAASFIEWFAEEA 123
              L +         D++A  ++LE G PL      A+A+   G    A S  + +A E 
Sbjct: 68  LEILAKVTAGYERRLDEIAEAISLEMGAPLERLAKPAQARAGLGHFKTALSLAKTYAFER 127

Query: 124 KRIYGDVIPGHQPDKRLIVIKQPIGVTAAITPWNFPAAMITRKAGPALAAGCTMVLKPAS 183
           ++               +V+K+P+GV + ITPWN+P   I  K  PALAAGC MVLKP+ 
Sbjct: 128 RQ------------GTTLVVKEPVGVVSLITPWNWPMNQIACKVAPALAAGCAMVLKPSE 175

Query: 184 QTPYSAFALAELAQRAGIPKGVLSVVTGSAGDIGSELTSNPIVRKLSFTGSTEIGRQLMA 243
             PYSA  LAE+   AG+P GV ++V G   +IG  L+S+P+V  +S TGS   G  +M 
Sbjct: 176 FAPYSARILAEIIHEAGVPAGVFNMVFGDGAEIGPVLSSHPLVDMVSLTGSNLAGSSVMR 235

Query: 244 ECAKDIKKVSLELGGNAPFIVFDDADLDKAVEGAIISKYRNNGQTCVCANRLYIQDSVYD 303
           E A  IKKVSLELGG +  I+ D AD  KA+  A+ +   N GQ+C   +RL++     D
Sbjct: 236 EGAATIKKVSLELGGKSANIICDSADFKKAIGHAVKAMMGNTGQSCNAPSRLFVPAHRLD 295

Query: 304 AFAEKLKVAVAKLKIGNGLEEGTTTGPLIDGKAVAKVQEHIADALSKGATLLAGGK---- 359
                     A++K+G+  +  T  GP+ +G+   KV+  I   + +GA L+ GG     
Sbjct: 296 EAEGLAAELCAQIKVGDPSDPETVMGPIANGRQFDKVRRMIRTGMEEGAKLVCGGPERPE 355

Query: 360 -VMEGNFFEPTILTNVPKSAAVAKEETFGPLAPLFRFKDEAEVIAMSNDTEFGLASYFYA 418
            + +G F  PT+ + V  +  + +EE FGP+  +  + D  + +A +ND  +GL+ Y YA
Sbjct: 356 GLDKGYFVRPTVFSRVTDAMTIMREEIFGPVLSMRGYADLDDAVAGANDCVYGLSGYVYA 415

Query: 419 RDLGRVFRVAEALEYGMVGVNTGLISNEVAPFGGIKASGLGREGSKYGIEDYLEIKYL 476
            DL     VA  L  GMV +N G +S+   PFGGI+ SG+GRE  + G E++LE K L
Sbjct: 416 GDLDEARAVARRLRTGMVHLN-GALSHPGGPFGGIRQSGVGREWGEAGFEEFLESKTL 472


Lambda     K      H
   0.317    0.135    0.389 

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: 574
Number of extensions: 24
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: 480
Length of database: 479
Length adjustment: 34
Effective length of query: 446
Effective length of database: 445
Effective search space:   198470
Effective search space used:   198470
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 (21.7 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 (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