GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mmsA in Shewanella loihica PV-4

Align methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized)
to candidate 5210745 Shew_3173 succinic semialdehyde dehydrogenase (RefSeq)

Query= BRENDA::P42412
         (487 letters)



>FitnessBrowser__PV4:5210745
          Length = 485

 Score =  265 bits (677), Expect = 3e-75
 Identities = 157/475 (33%), Positives = 258/475 (54%), Gaps = 8/475 (1%)

Query: 3   EIRKLKNYINGEWVESKTDQYEDVVNPATKEVLCQVPISTKEDIDYAAQTAAEAFKTWSK 62
           ++ KL +YI+G W     +Q  DVVNPA++EV+ QV  ++ +D   A   A  A   WSK
Sbjct: 8   QLIKLSSYIDGRWTVG--EQRFDVVNPASQEVIAQVVDASLDDTQEAILAAKRALPEWSK 65

Query: 63  VAVPRRARILFNFQQLLSQHKEELAHLITIENGKNTKEALGEVGRGIENVEFAAGAPSLM 122
            +   RA ++  +  L+ +H+E+L  L+T+E GK   EA GE+  G   +++ A     +
Sbjct: 66  RSANERAALMRKWFNLMMEHQEDLGRLLTLEQGKPLAEAKGEIAYGAAFIDWFAEEGKRV 125

Query: 123 MGDSLASIATDVEAANYRYPIGVVGGIAPFNFPMMVPCWMFPMAIALGNTFILKPSERTP 182
            GD++ + A D      + P+GVV  I P+NFP  +       A+A G TF+ +PS  TP
Sbjct: 126 YGDTIPAPANDKRILVIKQPVGVVASITPWNFPNAMIARKAAAALAAGCTFVARPSPLTP 185

Query: 183 LLTEKLVELFEKAGLPKGVFNVVYGAHDVVNG--ILEHPEIKAISFVGSKPVGEYVYKKG 240
           L    + EL E+AG+P GVFN+V G   V  G  + +HP++   +F GS  VG+ +  + 
Sbjct: 186 LSALAMAELAERAGIPAGVFNIVVGEDAVGMGKVLTQHPDVAKFTFTGSTAVGKILLAQC 245

Query: 241 SENLKRVQSLTGAKNHTIVLNDANLEDTVTNIVGAAFGSAGERCMACAVVTVEEGIADEF 300
           + ++K+V    G     IV +DA+++  V   + + + +AG+ C+    + V++G+A  F
Sbjct: 246 ATSVKKVSMELGGNAPFIVFDDADIDAAVQGALISKYRNAGQTCVCTNRIFVQKGVAAAF 305

Query: 301 MAKLQEKVADIKIGNGLDDGVFLGPVIREDNKKRTLSYIEKGLEEGARLVCDGRENVSDD 360
             K    VA++K+G+GL DGV +GP+I +D  +  L  ++  +  GA+LV  G+ +   +
Sbjct: 306 TEKFTAAVANLKLGDGLGDGVTVGPMISKDAVQNVLKLVDDTVASGAKLVTGGQPSELGE 365

Query: 361 GYFVGPTIFDNVTTEMTIWKDEIFAPVLSVIRVKNLKEAIEIANKSEFANGACLFTSNSN 420
             F+ P I  +VT EM + ++EIF PV  +I   +  EA+ +AN +E+   A  +  +  
Sbjct: 366 S-FLAPVIVTDVTNEMPLARNEIFGPVTPIISFDSEAEALAMANDTEYGLAAYFYARDIG 424

Query: 421 AIRYFRENIDAGMLGINLGVPAPMAFFPFSGWKSSFFGTLHANGKDSVDFYTRKK 475
            I    E ++ GM+G+N G+ +  A  PF G K S  G      K  +D Y   K
Sbjct: 425 RIFRVAEGLEYGMVGVNEGIISNAA-APFGGVKQS--GNGREGSKYGLDDYLEIK 476


Lambda     K      H
   0.318    0.136    0.396 

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: 546
Number of extensions: 27
Number of successful extensions: 3
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: 485
Length adjustment: 34
Effective length of query: 453
Effective length of database: 451
Effective search space:   204303
Effective search space used:   204303
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.

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