GapMind for catabolism of small carbon sources

 

Aligments for a candidate for pad-dh in Shewanella sp. ANA-3

Align long-chain-aldehyde dehydrogenase (EC 1.2.1.48) (characterized)
to candidate 7026109 Shewana3_3251 aldehyde dehydrogenase (RefSeq)

Query= BRENDA::P51648
         (485 letters)



>lcl|FitnessBrowser__ANA3:7026109 Shewana3_3251 aldehyde
           dehydrogenase (RefSeq)
          Length = 474

 Score =  296 bits (759), Expect = 8e-85
 Identities = 166/448 (37%), Positives = 261/448 (58%), Gaps = 15/448 (3%)

Query: 5   VRRVRQAFLSGRSRPLRFRLQQLEALRRMVQEREKDILTAIAADLC-KSEFNVYSQEVIT 63
           ++R R ++L+  +     R ++L  L+  + + ++ ++ A++ D   +S  +    +++ 
Sbjct: 17  LQRQRASYLAAPNPDYAIRKERLLRLKAALLKFQQPLVEALSQDYGHRSVDDSLISDIMP 76

Query: 64  VLGEIDFMLENLPEWVTAKPVKKNVLTMLDEAYIQP--QPLGVVLIIGAWNYPFVLTIQP 121
           V+  I++ L+NL +W+  KP +++   +L  A ++   QPLGV+ II  WN+P +L+I P
Sbjct: 77  VVNNINYSLKNLKKWL--KPSRRHAGILLAPAQVKVHYQPLGVIGIIVPWNFPVMLSIGP 134

Query: 122 LIGAIAAGNAVIIKPSELSENTAKILAKLLPQYLDQDLYIVINGGVEETTELLKQRFDHI 181
           L+ AIAAGN  ++K SE +  T  ++ +LL +  ++    V+ G  +   +     FDH+
Sbjct: 135 LVTAIAAGNHAMLKLSEFTPATNSVIKQLLAEVFEESHVAVVEGEADVAAQFSALPFDHL 194

Query: 182 FYTGNTAVGKIVMEAAAKHLTPVTLELGGKSPCYIDKDCDLDIVCRRITWGKYMNCGQTC 241
            +TG+T VG+ VM AAA +LTPVTLELGGKSP  I  D  L+I   R+ +GK +N GQ C
Sbjct: 195 LFTGSTTVGRHVMRAAANNLTPVTLELGGKSPVIIAPDMPLEIAVERMIYGKCLNAGQIC 254

Query: 242 IAPDYILCEASLQNQIVWKIKETVKEFYGENIKESPDYERIINLRHFKRILSLLEGQKI- 300
           +APDY+LC  +   + +   +   +  YG  I  + DY  IIN R F+R+L++LE  K  
Sbjct: 255 VAPDYVLCPKAKVAEFIQAYQAKFQAMYGA-ITHNKDYGSIINARQFERLLTVLEDAKAK 313

Query: 301 ------AFGGETDEATRYIAPTVLTDVDPKTKVMQEEIFGPILPIVPVKNVDEAINFINE 354
                 A     D   R +A  ++TD      +MQEEIFGP+LP+    N+DEAI+++N 
Sbjct: 314 GAKVIPASNDVIDSQHRKLATQLITDTTEDMLLMQEEIFGPLLPVTGYDNLDEAISYVNH 373

Query: 355 REKPLALYVFSHNHKLIKRMIDETSSGGVTGNDVIMHFTLNSFPFGGVGSSGMGAYHGKH 414
           R +PLALYV S +    ++++ +T SGGV  N+ + H   +  PFGG+G SGMG YHGK 
Sbjct: 374 RARPLALYVMSFDEASQQKILKQTHSGGVCINETVFHVAADDAPFGGIGPSGMGHYHGKE 433

Query: 415 SFDTFSHQRPCLLKSLKREGANKLRYPP 442
            F TFSH +  L  S  R    K  +PP
Sbjct: 434 GFLTFSHAKTVL--SRGRFNTGKFVHPP 459


Lambda     K      H
   0.321    0.139    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: 536
Number of extensions: 20
Number of successful extensions: 3
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: 485
Length of database: 474
Length adjustment: 34
Effective length of query: 451
Effective length of database: 440
Effective search space:   198440
Effective search space used:   198440
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 (21.9 bits)
S2: 51 (24.3 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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