GapMind for catabolism of small carbon sources

 

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

Align aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized)
to candidate WP_011383257.1 AMB_RS04160 NAD-dependent succinate-semialdehyde dehydrogenase

Query= BRENDA::C6KEM4
         (506 letters)



>NCBI__GCF_000009985.1:WP_011383257.1
          Length = 499

 Score =  291 bits (746), Expect = 3e-83
 Identities = 179/479 (37%), Positives = 268/479 (55%), Gaps = 16/479 (3%)

Query: 13  FIGGAWREPCLGRRLPVVNPATEATIGDIPAGTAEDVEIAVAAARDAFSRDGGRQWSRAP 72
           ++ G W     GRR  V++PAT   I  +P   A +   A+ AA  A++      W +  
Sbjct: 28  YVDGVWVGADDGRRFDVLDPATGGLIASVPDLGATETRRAIDAAEAAWN-----PWRQRT 82

Query: 73  GAVRANFLRAIAAKIKDRKSELALLETLDSGKPLDEASGDMDDVAACFEYYADLAEALDG 132
              RA  + A    I   +  LA L + + GKPL EA G++   A+   ++A+     +G
Sbjct: 83  AKDRAAVMMAWHDLIMAHQDALARLLSAEQGKPLAEAMGEISYGASFISWFAE-----EG 137

Query: 133 KQRSPISLPM--ENFKSYVLKEPIGVVGLITPWNYPLLMATWKVAPALAAGCTTILKPSE 190
           K+     +P    + +  V+K+PIGVV  +TPWN+P+ M T K APALAAGC  ++KP+E
Sbjct: 138 KRAYGDLIPTTASDRRLLVMKQPIGVVAAVTPWNFPMAMITRKCAPALAAGCPVVVKPAE 197

Query: 191 LASVSCLELGAICMEIGLPPGVLNIITGLGPEA-GAPLSSHSHVDKVAFTGSTETGKRIM 249
              +S L L  +    GLP G+ NI+T   P A G  ++ ++ V K++FTGST  GK +M
Sbjct: 198 DTPLSALALAELAHRAGLPKGLFNIVTTRQPAAVGGEMTGNAKVRKLSFTGSTRVGKLLM 257

Query: 250 TSAAQMVKPVSLELGGKSPLIVFDDIGDIDKAVEWTMFGIFANAGQVCSATSRLLLHEKI 309
              A+ VK VSLELGG +P IVFDD  D+D AV   +   + N+GQ C  T+R L+   I
Sbjct: 258 AQCAETVKKVSLELGGNAPFIVFDDC-DLDAAVAGALASKYRNSGQTCICTNRFLVQAGI 316

Query: 310 AKKFLDRLVAWAKNIKVSDPLEEGCRLGSVISEGQYEKIKKFISTARSEGATILYGGGRP 369
            + F  +L   A  + V   L    + G +I+     K+   ++ A S+GA +L GG RP
Sbjct: 317 YEDFAVKLAEKAAAMAVGHALSGVVQQGPLINAAAVAKVAAHVADAVSKGARVLTGG-RP 375

Query: 370 QHLRRGFFLEPTIITDVSTSMQIWQEEVFGPVICVKEFRTDSEAVELANDTHYGLAGAVI 429
             L  GF+ +PT++ DV+ +M  ++EE FGPV  +  F T++EA+ LAN + +GLAG   
Sbjct: 376 HALGGGFW-QPTVLADVTPAMLCFREETFGPVAPLLRFETEAEAIALANASEFGLAGYFY 434

Query: 430 SNDQERCERISKALHSGIIWINCSQPCFVQAPWGGNKRSGFGRELGEWGLDNYLTVKQV 488
           S D  R  R+++AL  G++ +N S      AP+GG K SG GRE  ++GLD+++  K V
Sbjct: 435 SRDVARVFRVAEALECGMVGVNESLISNEVAPFGGIKESGLGREGSKYGLDDFMETKYV 493


Lambda     K      H
   0.318    0.136    0.418 

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: 654
Number of extensions: 41
Number of successful extensions: 6
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: 506
Length of database: 499
Length adjustment: 34
Effective length of query: 472
Effective length of database: 465
Effective search space:   219480
Effective search space used:   219480
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: 52 (24.6 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