GapMind for catabolism of small carbon sources

 

Alignments 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)



>NCBI__GCF_000009985.1:WP_011385299.1
          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:

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