GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|NCBI__GCF_000009985.1:WP_011384974.1 AMB_RS13050 aldehyde
           dehydrogenase family protein
          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 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