GapMind for catabolism of small carbon sources

 

Alignments for a candidate for iolA in Shewanella sp. ANA-3

Align malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized)
to candidate 7025959 Shewana3_3107 methylmalonate-semialdehyde dehydrogenase [acylating] (RefSeq)

Query= reanno::pseudo6_N2E2:Pf6N2E2_515
         (500 letters)



>FitnessBrowser__ANA3:7025959
          Length = 496

 Score =  635 bits (1637), Expect = 0.0
 Identities = 304/490 (62%), Positives = 381/490 (77%), Gaps = 1/490 (0%)

Query: 9   HYLNGHVQDHDSTRFSNVFNPATGAVQARVALAEPGTVDAAVASALAAFPAWSEQSSLRR 68
           HY+NG      STR   +F PATG  + +V+LA    V AA+A A +AF  WS+ + L R
Sbjct: 6   HYVNGE-HTAASTRSQEIFEPATGECRGQVSLASRDEVSAAIAIAKSAFDTWSQVTPLNR 64

Query: 69  SRVMFKFKELLDRHHDELAQIISREHGKVLSDAHGEVTRGIEIVEYACGAPNLLKTDFSD 128
           +RV+FKFK L+++H DELAQ+I+ EHGKVL DA GE+ RG+E+VE+ACG P+LLK + ++
Sbjct: 65  ARVLFKFKALVEQHMDELAQLITLEHGKVLDDARGELIRGLEVVEFACGIPHLLKGEHTE 124

Query: 129 NIGGGIDNWNLRQPLGVCAGVTPFNFPVMVPLWMIPLALVAGNCFILKPSERDPSASLLM 188
            +GGG+D W++ Q LGV AG+ PFNFPVMVP+WM P+A+  GN FI+KPSE+DPSA + +
Sbjct: 125 QVGGGVDAWSVNQALGVVAGIAPFNFPVMVPMWMFPIAIACGNTFIMKPSEKDPSAVMRI 184

Query: 189 ARLLTEAGLPDGVFNVVQGDKVAVDALLQHPDIEAISFVGSTPIAEYIHQQGTAHGKRVQ 248
           A LLT+AGLP GVFNVV GDK AVD LL H DI+A+SFVGSTPIAEYI+   + HGKRVQ
Sbjct: 185 AELLTQAGLPAGVFNVVNGDKEAVDTLLSHEDIQAVSFVGSTPIAEYIYSTASKHGKRVQ 244

Query: 249 ALGGAKNHMIVMPDADLDQAADALIGAAYGSAGERCMAISIAVAVGDVGDELIAKLLPRI 308
           ALGGAKNHM++MPDADLDQA  AL+GAAYGSAGERCMAIS+ +AVGDVGD+L+ KLLP+I
Sbjct: 245 ALGGAKNHMLLMPDADLDQAVSALMGAAYGSAGERCMAISVVLAVGDVGDKLVDKLLPQI 304

Query: 309 DQLKIGNGQQPGTDMGPLVTAEHKAKVEGFIDAGVAEGARLIVDGRSFKVPGAEQGFFVG 368
            QLK+GNG  P  +MGPL++ +H AKV  F+DAGV EGA L+VDGR   V   +QG+F+G
Sbjct: 305 QQLKVGNGLTPEMEMGPLISRQHLAKVTEFVDAGVKEGATLVVDGRQLTVADHQQGYFLG 364

Query: 369 ATLFDQVTAEMSIYQQEIFGPVLGIVRVPDFATAVALINAHEFGNGVSCFTRDGGIARAF 428
           A LFD VT EM IY++EIFGPVL IVRV D+A+A+ALIN HEFGNG + FT+ G  AR F
Sbjct: 365 ACLFDNVTPEMRIYREEIFGPVLSIVRVKDYASALALINQHEFGNGTAIFTQSGEAARHF 424

Query: 429 ARSIKVGMVGINVPIPVPMAWHSFGGWKRSLFGDHHAYGEEGLRFYSRYKSVMQRWPDSI 488
              ++VGMVG+NVPIPVPMA+HSFGGWKRSLFG  H +G +G+RFY++ K++  RWP   
Sbjct: 425 CHHVQVGMVGVNVPIPVPMAFHSFGGWKRSLFGPLHMHGPDGVRFYTKRKAITARWPVGK 484

Query: 489 AKGPEFSMPT 498
               EF MPT
Sbjct: 485 QTQAEFVMPT 494


Lambda     K      H
   0.321    0.137    0.415 

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: 686
Number of extensions: 21
Number of successful extensions: 1
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: 500
Length of database: 496
Length adjustment: 34
Effective length of query: 466
Effective length of database: 462
Effective search space:   215292
Effective search space used:   215292
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