GapMind for catabolism of small carbon sources

 

Alignments for a candidate for iolA in Psychromonas ingrahamii 37

Align malonate-semialdehyde dehydrogenase (EC 1.2.1.15); malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18); methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized)
to candidate WP_011771045.1 PING_RS14365 NAD-dependent succinate-semialdehyde dehydrogenase

Query= BRENDA::A0A081YAY7
         (498 letters)



>NCBI__GCF_000015285.1:WP_011771045.1
          Length = 481

 Score =  221 bits (564), Expect = 3e-62
 Identities = 143/479 (29%), Positives = 244/479 (50%), Gaps = 12/479 (2%)

Query: 6   HLIGGELIADTGRTADVFNPSTGEAVRKVPLADRETMQQAIDAAKAAFPAWRNTPPAKRA 65
           ++ G  ++  T  T +V+NP+  E +  V  A  E +  AI+AA  AF  WR   P +RA
Sbjct: 12  YINGQFILTATKTTFNVYNPANNECLASVENAGEEEVVNAINAADQAFALWRTVAPRERA 71

Query: 66  QVLFRFKQLLEANEERIVKLISEEHGKTIEDAAGELKRGIENVEYATAAPEILKGEYSRN 125
           ++L     ++  N+E I  LIS E GKT+ ++ GE+    E   + +     + G+ SR+
Sbjct: 72  EILRSCYNIMIKNKENIANLISLEEGKTLSESLGEVNYAAEFFRWFSEEAVRINGDLSRS 131

Query: 126 VGPNIDAWSDFQPIGVVAGITPFNFPAMVPLWMYPLAIACGNTFILKPSERDPSSTLLIA 185
              N +     +P+G+   ITP+NFPA +       A+A G + I+KPSE  P + L +A
Sbjct: 132 PSGNNNILVTNEPVGICYLITPWNFPAAMMTRKIAPALAAGCSVIVKPSEETPLTALYLA 191

Query: 186 ELFHEAGLPKGVLNVVHGDK--GAVDALIEAPEVKALSFVGSTPIAEYIYSEGTKRGKRV 243
           +LF EAG+PKG++NV+  ++     +A+ +   ++ +SF GST I  ++ S+ +K+    
Sbjct: 192 QLFSEAGVPKGLINVLPSNRPEELSEAIFKDNRIRKISFTGSTNIGSHLLSKASKKVVNC 251

Query: 244 QALGGAKNHAVLMPDADLDNAVSALMGAAYGSCGERCMAISVAVCVGDQIADALVQKLVP 303
               G     +++ DADLD A+ + M A   + GE C+A +    V   +A +  +KL  
Sbjct: 252 SMELGGNAPFIVLDDADLDVAIDSAMIAKMRNAGESCIAAN-RFYVHQSLAASFTEKLTK 310

Query: 304 QIKGLKIGAGTSCGLDMGPLVTGAARDKVTGYIDTGVAQGAELVVDGRGYKVAGHENGFF 363
           ++  LK+G G     D+GPL+   A  KV G +   + +GA+L   G   +     +  +
Sbjct: 311 KMAVLKVGNGLDSTTDVGPLINRKAVIKVDGLVQEAIKKGAKLHCGGGLIE----SDSCY 366

Query: 364 LGGTLFDRVTPEMTIYKEEIFGPVLCIVRVNSLEEAMQLINDHEYGNGTCIFTRDGEAAR 423
              T+   +  +  I+ +EIFGPV  I   + ++  +   N+ ++G    I + D + A 
Sbjct: 367 YSPTVLSNIPKDADIFSQEIFGPVAAISTFDDIDSVISSANNTDFGLAAYIISADIKKAL 426

Query: 424 LFCDEIEVGMVGVNVP-LPVPVAYHSFGGWKRSLFGDLHAYGPDGVRFYTKRKAITQRW 481
                +E G++G+N   +  P A   FGG K+S  G     G DG+  + ++K I   W
Sbjct: 427 RVASLLEAGVIGINQGFISDPAA--PFGGVKQSGLG--REGGGDGIWEFIEKKYIAVDW 481


Lambda     K      H
   0.319    0.137    0.411 

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: 527
Number of extensions: 24
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: 498
Length of database: 481
Length adjustment: 34
Effective length of query: 464
Effective length of database: 447
Effective search space:   207408
Effective search space used:   207408
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 (21.7 bits)
S2: 52 (24.6 bits)

This GapMind analysis is from Sep 24 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