GapMind for catabolism of small carbon sources

 

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

Align 2-aminomuconic semialdehyde dehydrogenase; Aldehyde dehydrogenase 12; Aldehyde dehydrogenase family 8 member A1; EC 1.2.1.32 (characterized)
to candidate WP_011384974.1 AMB_RS13050 aldehyde dehydrogenase family protein

Query= SwissProt::Q9H2A2
         (487 letters)



>NCBI__GCF_000009985.1:WP_011384974.1
          Length = 479

 Score =  271 bits (694), Expect = 3e-77
 Identities = 167/483 (34%), Positives = 262/483 (54%), Gaps = 24/483 (4%)

Query: 10  LENFIDGKFLPC---SSYIDSYDPSTGEVYCRVPNSGKDEIEAAVKAAREAFPSWSSRSP 66
           L+ ++DG ++     S  +D  +P+T +V  RV   G D+   A++AA +AFP+W++   
Sbjct: 5   LDFYVDGAWVKPAKGSRLLDVINPATEQVSGRVALGGADDAVRAIQAAAKAFPAWAATPL 64

Query: 67  QERSRVLNQVADLLEQSLEEFAQAESKDQGKTLA-LARTMDIPRSVQNFRFFASSSLHHT 125
            ER  +L +V    E+ L+E A+A S + G  L  LA+       + +F+   S +  + 
Sbjct: 65  AERLEILAKVTAGYERRLDEIAEAISLEMGAPLERLAKPAQARAGLGHFKTALSLAKTYA 124

Query: 126 SECTQMDHLGCMHYTVRAPVGVAGLISPWNLPLYLLTWKIAPAMAAGNTVIAKPSELTSV 185
            E  Q   L      V+ PVGV  LI+PWN P+  +  K+APA+AAG  ++ KPSE    
Sbjct: 125 FERRQGTTL-----VVKEPVGVVSLITPWNWPMNQIACKVAPALAAGCAMVLKPSEFAPY 179

Query: 186 TAWMLCKLLDKAGVPPGVVNIVFGTGPRVGEALVSHPEVPLISFTGSQPTAERITQLSAP 245
           +A +L +++ +AGVP GV N+VFG G  +G  L SHP V ++S TGS      + +  A 
Sbjct: 180 SARILAEIIHEAGVPAGVFNMVFGDGAEIGPVLSSHPLVDMVSLTGSNLAGSSVMREGAA 239

Query: 246 HCKKLSLELGGKNPAIIFEDANLDECIPATVRSSFANQGEICLCTSRIFVQKSIYSEFLK 305
             KK+SLELGGK+  II + A+  + I   V++   N G+ C   SR+FV      E   
Sbjct: 240 TIKKVSLELGGKSANIICDSADFKKAIGHAVKAMMGNTGQSCNAPSRLFVPAHRLDEAEG 299

Query: 306 RFVEATRKWKVGIPSDPLVSIGALISKAHLEKVRSYVKRALAEGAQIWCG-----EGVDK 360
              E   + KVG PSDP   +G + +    +KVR  ++  + EGA++ CG     EG+DK
Sbjct: 300 LAAELCAQIKVGDPSDPETVMGPIANGRQFDKVRRMIRTGMEEGAKLVCGGPERPEGLDK 359

Query: 361 LSLPARNQAGYFMLPTVITDIKDESCCMTEEIFGPVTCVVPFDSEEEVIERANNVKYGLA 420
                    GYF+ PTV + + D    M EEIFGPV  +  +   ++ +  AN+  YGL+
Sbjct: 360 ---------GYFVRPTVFSRVTDAMTIMREEIFGPVLSMRGYADLDDAVAGANDCVYGLS 410

Query: 421 ATVWSSNVGRVHRVAKKLQSGLVWTNCWLIRELNLPFGGMKSSGIGREGAKDSYDFFTEI 480
             V++ ++     VA++L++G+V  N   +     PFGG++ SG+GRE  +  ++ F E 
Sbjct: 411 GYVYAGDLDEARAVARRLRTGMVHLN-GALSHPGGPFGGIRQSGVGREWGEAGFEEFLES 469

Query: 481 KTI 483
           KT+
Sbjct: 470 KTL 472


Lambda     K      H
   0.319    0.133    0.404 

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: 532
Number of extensions: 27
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: 487
Length of database: 479
Length adjustment: 34
Effective length of query: 453
Effective length of database: 445
Effective search space:   201585
Effective search space used:   201585
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 (21.8 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