GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mmsA in Pedobacter sp. GW460-11-11-14-LB5

Align Malonate-semialdehyde dehydrogenase 1; MSA dehydrogenase 1; EC 1.2.1.-; Methylmalonate-semialdehyde dehydrogenase 1; MMSA dehydrogenase 1; MSDH 1; EC 1.2.1.27 (uncharacterized)
to candidate CA265_RS19780 CA265_RS19780 aldehyde dehydrogenase family protein

Query= curated2:Q5L025
         (488 letters)



>FitnessBrowser__Pedo557:CA265_RS19780
          Length = 513

 Score =  202 bits (513), Expect = 3e-56
 Identities = 148/482 (30%), Positives = 234/482 (48%), Gaps = 17/482 (3%)

Query: 16  GGQWVASSGTETLEVPNPATGEVLARVPISTKEDVDQAVQAAKKAFATWKDVPVPKRARI 75
           G  W       TLE  +P  G+++A   I+T +D D  V  A++AF  W+ VP PKR  I
Sbjct: 24  GSNWGGELNVNTLESFSPVDGKLIASAKIATADDYDAVVLKAQEAFTAWRSVPAPKRGEI 83

Query: 76  MFSFHHLLNQHHEELAELVVQENGKAYKEAYGEIQRGIECVEFAAGAPTLLMGESLSNIA 135
           +  F   L ++ + L  LV  E GK+ +E +GE+Q  I+  +FA G    L G  L+  +
Sbjct: 84  VRQFGDALRENKDALGTLVSYEMGKSLQEGFGEVQEMIDICDFAVGLSRQLYG--LTMHS 141

Query: 136 EEIDSEMFR--YPLGVVAGITPFNFPMMVPLWMFPLAIVCGNTFVLKPSERTPILA---- 189
           E     M+   +PLG+V  I+ FNFP+ V  W   LA+VCGN  + KPSE+TP+ A    
Sbjct: 142 ERPSHRMYEQWHPLGIVGIISAFNFPVAVWSWNTALALVCGNVCIWKPSEKTPLTAIACQ 201

Query: 190 NKLAELFTEAGAPPGVLNVVHGAHEVVNALIDHEDIRAISFVGSQPVAKYVYERTAAQ-G 248
           + +A++F +     GV N++ G  EV   + +   I  IS  GS  + K V     A+ G
Sbjct: 202 HIIAKVFKDNDIAEGVCNLILGDREVGERMTNDGRIPLISATGSTRMGKAVGAAVGARLG 261

Query: 249 KRVQALSGAKNHHIVMPDADVETAVQHVISSAFGSAGQRCMACSAVVI-VGENETFVRRL 307
           K +  L G  N  I+   AD++ ++   +  A G+AGQRC +   ++I     + F  +L
Sbjct: 262 KSLLEL-GGNNAIIISEHADLDMSLIGAVFGAVGTAGQRCTSTRRLIIHESVYDAFTAKL 320

Query: 308 KQKADELIIGNGMDPEVLLTPVIRQSHREKVLGYIQK-GIEEGAVLLRDGRKEMDDRPEG 366
            +   +L IG+ +D    + P+I        L  I K   E G  ++  G    D    G
Sbjct: 321 VKAYGQLRIGDPLDQNNHVGPLIDTDAVAAYLDSIAKCKAEGGNFVVEGGVLSGDAYTSG 380

Query: 367 NFLGPTIFDYVTPDMTIAKEEIFAPVLSLLRANDLDEALSYIRKSRYGNGATIYTKDAKA 426
            ++ P I + V  D  I + E FAP+L L++   LDEA++       G  + I T + + 
Sbjct: 381 CYVKPCIAE-VQNDFKIVQHETFAPILYLIKYKTLDEAIALQNGVPQGLSSAIMTLNLRE 439

Query: 427 VRKF--REEADAGMLGINVGVPATMAFFPFSGWKDSFYGDLHVNGKDGVNFYTRKKMITS 484
             +F   + +D G+  +N+G         F G K++  G    +G D    Y R++  T 
Sbjct: 440 AEQFLSAKGSDCGIANVNIGTSGAEIGGAFGGEKET--GGGRESGSDAWRAYMRRQTNTI 497

Query: 485 RF 486
            +
Sbjct: 498 NY 499


Lambda     K      H
   0.319    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: 549
Number of extensions: 31
Number of successful extensions: 4
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: 488
Length of database: 513
Length adjustment: 34
Effective length of query: 454
Effective length of database: 479
Effective search space:   217466
Effective search space used:   217466
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