GapMind for catabolism of small carbon sources

 

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

Align Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- (characterized)
to candidate 5208455 Shew_0967 aldehyde dehydrogenase (RefSeq)

Query= SwissProt::Q9I6M5
         (483 letters)



>FitnessBrowser__PV4:5208455
          Length = 498

 Score =  285 bits (730), Expect = 2e-81
 Identities = 170/482 (35%), Positives = 267/482 (55%), Gaps = 8/482 (1%)

Query: 2   QLKDAKLFRQQAYVDGAWVDADNGQTIKVNNPATGEIIGSVPKMGAAETRRAIEAADKAL 61
           ++ D+ + + QA+++G +  AD+  T    +P  G ++  V      +  RA+  A +  
Sbjct: 12  EMADSLVIQGQAFINGEYCAADSNDTFDCISPIDGRVLTQVASCDLLDANRAVANAREVF 71

Query: 62  PA--WRALTAKERANKLRRWFDLMIENQDDLARLMTIEQGKPLAEAKG-EIAYAASFLEW 118
               W  L   +R   + R+ DL+  N+D+LA L T++ GKP+  +   ++A AA  L W
Sbjct: 72  ERGDWSQLPPVKRKQVMIRFADLLEANRDELALLETLDMGKPIRYSGAVDVAGAARALRW 131

Query: 119 FGEEAKRIYGDTIPGHQPDKRIIVIKQPIGVTAAITPWNFPSAMITRKAGPALAAGCTMV 178
            GE   +IY +  P    +  +I  ++P+GV AAI PWNFP  M   K GPALA G ++V
Sbjct: 132 SGEAVDKIYDEIAPTAHNEIGMIT-REPVGVVAAIVPWNFPLLMACWKLGPALATGNSVV 190

Query: 179 LKPASQTPYSALALAELAERAGIPKGVFSVVTGSAGEVGGELTSNPIVRKLTFTGSTEIG 238
           LKP+ ++P +A+ +A+LA  AGIPKGV +V+ G    VG  L  +  V  L FTGST+I 
Sbjct: 191 LKPSEKSPLTAIRMAQLAIEAGIPKGVLNVLPGYGHTVGKALALHMDVDTLVFTGSTKIA 250

Query: 239 RQLMAECAQ-DIKKVSLELGGNAPFIVFDDA-DLDAAVEGALISKYRNNGQTCVCANRLY 296
           +QLM    + ++K+V LE GG +P IVF+DA +L  A   A  +   N G+ C   +RL 
Sbjct: 251 KQLMIYAGESNMKRVWLEAGGKSPNIVFNDAPNLKEAAIAAASAIAFNQGEVCTAGSRLL 310

Query: 297 VQDGVYDAFVDKLKAAVAKLNIGNGLEAGVTTGPLIDAKAVAKVEEHIADAVSKGAKVVS 356
           V+ GV +  ++ ++A +     G+ L+   T G ++D + +  V  +I   V++GA++  
Sbjct: 311 VESGVKEELINLIEAEMQAWQPGHPLDPATTCGAVVDQQQLENVLRYIRAGVAEGAQLRQ 370

Query: 357 GGKP--HALGGTFFEPTILVDVPKNALVSKDETFGPLAPVFRFKDEAEVIAMSNDTEFGL 414
           GG+      GG +  PTI  +V     ++K+E FGP+  V  F    E I + NDT +GL
Sbjct: 371 GGQQVLAETGGVYVAPTIFANVKNEMTIAKEEIFGPVLSVITFDGMEEAIRIGNDTIYGL 430

Query: 415 ASYFYARDLARVFRVAEQLEYGMVGINTGLISNEVAPFGGIKASGLGREGSKYGIEDYLE 474
           A+  +  D+++  + A+ L  GMV IN     +  APFGG K SG GR+ S +  + Y E
Sbjct: 431 AAGVWTSDISKAHKTAKALRSGMVWINHYDGGDMTAPFGGYKQSGNGRDKSLHAFDKYTE 490

Query: 475 IK 476
           IK
Sbjct: 491 IK 492


Lambda     K      H
   0.317    0.135    0.391 

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: 582
Number of extensions: 36
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: 483
Length of database: 498
Length adjustment: 34
Effective length of query: 449
Effective length of database: 464
Effective search space:   208336
Effective search space used:   208336
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.

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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