GapMind for catabolism of small carbon sources

 

Alignments for a candidate for iolA in Shewanella amazonensis SB2B

Align malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized)
to candidate 6938545 Sama_2648 aldehyde dehydrogenase (RefSeq)

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



>FitnessBrowser__SB2B:6938545
          Length = 498

 Score =  234 bits (596), Expect = 7e-66
 Identities = 162/484 (33%), Positives = 248/484 (51%), Gaps = 21/484 (4%)

Query: 10  YLNGHVQDHDSTRFSNVFNPATGAVQARVALAEPGTVDAAVASALAAFPA--WSEQSSLR 67
           ++NGH  D       +  +P  G +  +VA  +    D AVA+A A F +  WS QS ++
Sbjct: 24  FINGHYCDAVGKETFDCISPVDGRLLTQVASCQQADADIAVANARAVFESGVWSLQSPVK 83

Query: 68  RSRVMFKFKELLDRHHDELAQIISREHGKVLSDAHG-EVTRGIEIVEYACGAPNLLKTDF 126
           R +VM +F ELL+ H DELA + + + GK ++ +   +V      + ++  A + +  + 
Sbjct: 84  RKKVMIRFAELLEAHADELALLETLDMGKPIAHSKAVDVAGAARAIRWSGEAIDKIYDEL 143

Query: 127 SDNIGGGIDNWNLRQPLGVCAGVTPFNFPVMVPLWMIPLALVAGNCFILKPSERDPSASL 186
           +      I     R+P+GV A + P+NFP+++  W +  AL  GN  +LKPSE+ P  ++
Sbjct: 144 APTPHNEI-GMITREPVGVVAAIVPWNFPMLMACWKLGPALATGNSVVLKPSEKSPLTAI 202

Query: 187 LMARLLTEAGLPDGVFNVVQGDKVAV-DALLQHPDIEAISFVGSTPIAEYIH-QQGTAHG 244
            MA+L  EAGLPDGV NV+ G    V  AL  H D++ + F GST IA+ +    G ++ 
Sbjct: 203 RMAQLAKEAGLPDGVLNVLPGFGHTVGQALALHMDVDTLVFTGSTKIAKQLMVYAGQSNM 262

Query: 245 KRVQALGGAKNHMIVMPDA-DLDQAADALIGAAYGSAGERCMAISIAVAVGDVGDELIAK 303
           KRV    G K+  IV  DA DL  AA+A   A   + GE C A S  +    V DELI  
Sbjct: 263 KRVWLEAGGKSPNIVFNDAPDLKAAAEAAASAIAFNQGEVCTAGSRLLVESGVKDELIKL 322

Query: 304 LLPRIDQLKIGNGQQPGTDMGPLVTAEHKAKVEGFIDAGVAEGARLIVDGRSFKVPGAEQ 363
           ++  ++  + G+   P T  G +V  +    V G+I AG  EGA+L+  G   +V     
Sbjct: 323 IVKEMEAWQPGHPLDPATTCGAVVDKQQLDTVLGYIKAGHDEGAKLMCGGS--QVLAETG 380

Query: 364 GFFVGATLFDQVTAEMSIYQQEIFGPVLGIVRVPDFATAVALINAHEFGNGVSCFTRDGG 423
           G +V  T+FD VT +M I ++EIFGPV+ ++       AVA+ N   +G     +T D  
Sbjct: 381 GVYVAPTVFDGVTNQMKIAREEIFGPVMSVITFDGMDEAVAIANDTIYGLAAGVWTSDIS 440

Query: 424 IARAFARSIKVGMVGINVPIPVPMAWHSFGGWKRSLFGDHHAYG---EEGLRFYSRYKSV 480
            A   A++++ GMV IN         H  GG   + FG +   G   ++ L  + +Y  V
Sbjct: 441 KAHKTAKALRSGMVWIN---------HYDGGDMTAPFGGYKQSGNGRDKSLHAFEKYTEV 491

Query: 481 MQRW 484
              W
Sbjct: 492 KATW 495


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: 560
Number of extensions: 26
Number of successful extensions: 6
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: 498
Length adjustment: 34
Effective length of query: 466
Effective length of database: 464
Effective search space:   216224
Effective search space used:   216224
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