GapMind for catabolism of small carbon sources

 

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

Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized)
to candidate 5211158 Shew_3574 aldehyde dehydrogenase (RefSeq)

Query= BRENDA::Q9K9B2
         (515 letters)



>FitnessBrowser__PV4:5211158
          Length = 506

 Score =  223 bits (567), Expect = 2e-62
 Identities = 151/444 (34%), Positives = 231/444 (52%), Gaps = 27/444 (6%)

Query: 62  QLVGSVSKANQDLAEKAIQSADEAFQTWRNVNPEERANILVKAAAIIRRRKHEFSAWLVH 121
           Q+   V+++++   E A+ +A  A   W   +  ER+N+L+K A  + +     +     
Sbjct: 45  QVFCQVARSDERDIELALDAAHAAKDAWGKTSVTERSNLLLKIADRVEQNLEFLAVAETW 104

Query: 122 EAGKPWKEA-DADTAEAIDFLEYYARQMIELNRGKEILSRPGEQNRYFYTPMGVTVTISP 180
           E GK  +E  +AD    +D   Y+A   I    G          + +F  P+GV   I P
Sbjct: 105 ENGKAVRETLNADLPLFVDHFRYFAG-CIRAQEGSAADIDNNTVSYHFPEPLGVVGQIIP 163

Query: 181 WNFALAIMVGTAVAP-IVTGNTVVLKPASTTPVVAAKFVEVLEDAGLPKGVINYVPGSGA 239
           WNF L +M    +AP +  GN +VLKPA  TPV     VE+++D  LP GV+N V G G 
Sbjct: 164 WNFPL-LMAAWKIAPALAAGNCIVLKPAEQTPVSILVMVELIQDL-LPAGVLNIVNGFGT 221

Query: 240 EVGDYLVDHPKTSLITFTGSKDVGVRLYERAAVVRPGQNHLKRVIVEMGGKDT------V 293
           E G  L    + + + FTGS  +G  + + AA        L    VE+GGK        V
Sbjct: 222 EAGQALAVSKRIAKLAFTGSTQIGHHILKCAA------ESLIPSTVELGGKSPNIYFADV 275

Query: 294 VVDRDADLDLAAESILVSAFGFSGQKCSAGSRAVIHKDVYDEVLEKTVALAKNLTVGDPT 353
           +   D  LD A E +L++ F   G+ C+  SR +I + +YD+ ++K +A AK +  G+P 
Sbjct: 276 MEQEDEYLDKAVEGMLLAFFN-QGEVCTCPSRVLIAESIYDKFIDKVIARAKTIKQGNPL 334

Query: 354 NRDNYMGPVIDEKAFEKIMSYIEIGKKEG-RLMTGG-----EGDSSTGFFIQPTIIADLD 407
           + D  +G    ++ F+KI+SY+EIG+ EG  ++ GG      GD S+GF+I+PTI+   +
Sbjct: 335 DTDTQVGAQASQEQFDKILSYLEIGRNEGAEVLIGGTSCQLSGDQSSGFYIEPTILKGHN 394

Query: 408 PEAVIMQEEIFGPVVAFSKANDFDHALEIANNTEYGLTGAVITRNRAHIEQAKREFHVGN 467
            +  + QEEIFGPV++ +   D   AL IAN+TEYGL   V TR+    ++  R    G 
Sbjct: 395 -KMRVFQEEIFGPVISVTTFKDEAEALAIANDTEYGLGAGVWTRDMNRAQRMGRGIQAGR 453

Query: 468 LYFNRNCTGAIVGYHPFGGFKMSG 491
           ++   NC  A   +  FGG+K SG
Sbjct: 454 VWI--NCYHAYPAHAAFGGYKKSG 475


Lambda     K      H
   0.316    0.134    0.388 

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: 605
Number of extensions: 31
Number of successful extensions: 7
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: 515
Length of database: 506
Length adjustment: 35
Effective length of query: 480
Effective length of database: 471
Effective search space:   226080
Effective search space used:   226080
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 (21.6 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