GapMind for catabolism of small carbon sources

 

Aligments for a candidate for pfor in Magnetospirillum magneticum AMB-1

Align Aldehyde:ferredoxin oxidoreductase,tungsten-containing; EC 1.2.7.- (characterized, see rationale)
to candidate WP_011385299.1 AMB_RS14710 aldehyde ferredoxin oxidoreductase

Query= uniprot:Q5P143
         (616 letters)



>lcl|NCBI__GCF_000009985.1:WP_011385299.1 AMB_RS14710 aldehyde
           ferredoxin oxidoreductase
          Length = 616

 Score =  864 bits (2233), Expect = 0.0
 Identities = 414/617 (67%), Positives = 498/617 (80%), Gaps = 2/617 (0%)

Query: 1   MGWNRKVLRVNLAEGTCTPEPLNMQWADEYLGSRGLATKYLVSETDPKVDPLSPDNKMIM 60
           M W  K LR++L  G+   E LN  WA +YLG RGLATKY   E DPKVDPLSP NKMI 
Sbjct: 1   MSWTGKFLRIDLTNGSVKTEELNRAWARQYLGQRGLATKYFAEEVDPKVDPLSPANKMIF 60

Query: 61  ATGPLTGTMASTGGRYTVVTKGPLTGAIACSNSGGFFGAEMKFAGWDMVIFEGRSPTPVY 120
            TGPLTGT ASTGGRY+VVTKGPLT  IACSNSGGFFG E+K AGWDM+I EGRSP PVY
Sbjct: 61  TTGPLTGTAASTGGRYSVVTKGPLTNCIACSNSGGFFGNELKNAGWDMIIVEGRSPKPVY 120

Query: 121 LFIENERAELRDASYLWGRSCWETEESIRAQHQDPLIRVSSIGRAGENQVMFACIVNDLH 180
           L IENE  E+RDA+  WG++ WETE  ++A+HQDP++RV++IG AGE  V++ACIVNDLH
Sbjct: 121 LSIENETVEIRDAAEFWGKTVWETENGLKARHQDPMLRVATIGAAGEKGVLYACIVNDLH 180

Query: 181 RAAGRSGVGAVMGSKNLKAVAIRGTKGVSGIRDFPGFVRATSEAKKVLAGNPVTSEGLPK 240
           RAAGRSGVGAVMGSKNLKA+A+RGT+GV+ ++D   F++AT E KKVLA N VT +GLPK
Sbjct: 181 RAAGRSGVGAVMGSKNLKAIAVRGTRGVT-VKDPDRFIKATIEQKKVLADNAVTGQGLPK 239

Query: 241 FGTQVLMNVINEMGALPTRNHRDVQFEDASKISAEAMHEKRPSDGKPQLVTNAACFGCTI 300
           +GTQVLMNVINE+GA+PTRN ++VQFE A KISAEAMHE R +DGK  L TN ACFGCTI
Sbjct: 240 YGTQVLMNVINEIGAMPTRNFKEVQFEGAHKISAEAMHEPRATDGKANLATNGACFGCTI 299

Query: 301 ACGRISAIDKTHFTVKNNPKYWGASGGLEYEAAWALGAANGVGDLEALQYANLLCNEQGM 360
           ACGRIS +D  HF++ + P+Y   SGG+EYEAAWA+G+  GV DLEA  +AN +CNE G+
Sbjct: 300 ACGRISRMDPGHFSITSRPQYKEPSGGVEYEAAWAMGSDCGVDDLEACTFANFMCNEHGI 359

Query: 361 DPISFGATVGAAMELYETGVLTKERIG-LDAPFGSADALAKLAEMTATGEGFGKEIGLGS 419
           DPISFG+T+ AAME++E GV+TKE+ G ++  FGSA+AL K+AE+T  GEGFG E+G GS
Sbjct: 360 DPISFGSTLAAAMEMFEMGVITKEQTGGVELKFGSAEALVKMAELTGKGEGFGLELGQGS 419

Query: 420 KRLCEKYGHPELSMSVKGQEFPAYDSRGIQGMGLAYATSNRGACHLRGYTVASEVLGVPV 479
           +RLC KYGHPELSM+VK QEFPAYD RGIQGMGL YATSNRGACHLR YTVASEVLG+P 
Sbjct: 420 RRLCAKYGHPELSMTVKSQEFPAYDPRGIQGMGLTYATSNRGACHLRSYTVASEVLGIPF 479

Query: 480 KTDPHVIEGKAELVKAFQDATAVFDSAGICVFTSFAWTLADVQPQIAAACDGDWSMDKLA 539
           K+DP   +GKA LVKAFQDATA FD++GIC+FT+FAW+L ++ PQI AAC+G+W+ + L 
Sbjct: 480 KSDPLATDGKAALVKAFQDATAAFDASGICIFTTFAWSLENLAPQIDAACEGEWTPEILL 539

Query: 540 TVGERIWNMERQFNNAAGLGAQDDNLPPRLTSEPAKSGPAKGMVNRLAEMLPEYYGVRGW 599
            VGERIW +ERQFN AAG+ A DD LP RL  + AK+GPAKG+ + L +MLPEYY +RGW
Sbjct: 540 EVGERIWTLERQFNLAAGMTAADDTLPKRLLKDAAKTGPAKGLTSGLEKMLPEYYQLRGW 599

Query: 600 TPEGTPTPETLSRLGLS 616
           T +G PT ETL RL L+
Sbjct: 600 TTDGVPTTETLKRLQLA 616


Lambda     K      H
   0.316    0.133    0.404 

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: 1282
Number of extensions: 43
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: 616
Length of database: 616
Length adjustment: 37
Effective length of query: 579
Effective length of database: 579
Effective search space:   335241
Effective search space used:   335241
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: 53 (25.0 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 paper from 2022 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