GapMind for catabolism of small carbon sources

 

Alignments for a candidate for iorA in Magnetospirillum magneticum AMB-1

Align indolepyruvate ferredoxin oxidoreductase (subunit 2/2) (EC 1.2.7.8) (characterized)
to candidate WP_011385598.1 AMB_RS16325 4Fe-4S dicluster domain-containing protein

Query= BRENDA::Q6LZB6
         (578 letters)



>NCBI__GCF_000009985.1:WP_011385598.1
          Length = 618

 Score =  488 bits (1255), Expect = e-142
 Identities = 269/598 (44%), Positives = 384/598 (64%), Gaps = 29/598 (4%)

Query: 4   LMLGNEAVARGAYEAGVLVATAYPGTPSTEITEHISKYPEINSEWSVNEKVALEVAIGSA 63
           L+ GN+A+ARG +EAG  VA AYPGTPSTEI E +S YP++ +EWSVNEKVA+EVAIG +
Sbjct: 14  LLSGNDAIARGVWEAGAKVAAAYPGTPSTEILESLSLYPDLYAEWSVNEKVAMEVAIGGS 73

Query: 64  IAGARTVVSMKHVGLNVAADPLMTVAYTGINAGLLIIVADDPSMHSSQNEQDTRYYGIFS 123
           ++GAR+  +MKHVGLNVA+D  MTV   G+  GL+I VADD  M SSQNEQD+R++G F+
Sbjct: 74  MSGARSFCAMKHVGLNVASDAFMTVTVAGVIGGLVIAVADDVGMSSSQNEQDSRFWGRFA 133

Query: 124 KIPVLEPSDSQECKDFVKLGLEISEKFDTPVILRLSTRVSHSQSLVELEEKEKIELKPYD 183
            +PVLEP+DSQE  +  K   E+SE ++TPVILRL+TRV H +++V++ EK   ++  + 
Sbjct: 134 HVPVLEPADSQEAYEMAKYAFELSEAYNTPVILRLTTRVCHVKAVVQVGEKVAHDIGGFK 193

Query: 184 YNPSKYVSAPANAKKRRIFIEERLKELSNFADSSDVNKIEYA-NKKIGIITSGVAYNYAK 242
            +  ++V  PANAK        R  +L   A++S +N ++   +K++G +TSG AY + +
Sbjct: 194 SDARRWVMTPANAKGLLPAQIAREGKLQALAEASPMNFLDDGPDKRVGFVTSGPAYMHVR 253

Query: 243 EAVSDASFLKFGMSYPLPEEKIKEFVQNCDKVYVFEELEPIFEQKIRSMGLNVI-GKEIF 301
           E+  DA  LK G +YP+P   +++     + + V EE EP+ EQ++++ GL  I GK++ 
Sbjct: 254 ESFPDAPVLKLGFTYPVPVALVEKLAAQVEHLVVVEETEPLMEQELKAAGLQAIHGKDLL 313

Query: 302 PIVGELSSEIIRNAL---LNE---SKIVIEKIEDLPQRPPVLCPGCHHRGPFYVLKKLK- 354
           P +GEL+  ++  A+   L E         K +  P RPP +C  C H G +Y L +++ 
Sbjct: 314 PRLGELTPNVLIPAIKTFLGEPLPPTTTYPKFDPFP-RPPTMCAACPHMGVYYSLARMRK 372

Query: 355 -LHVAGDIGCYTLGGFEPLNAIDTTICMGASIGMAHGFEMARGKEFAKKS-VAVIGDSTF 412
            + ++GDIGCYTLG   P NA+D+TI MGAS+G+A G + AR +E   K+ VAVIGDSTF
Sbjct: 373 NVQISGDIGCYTLGAGHPWNALDSTISMGASMGIALGMDKARTEETKDKAVVAVIGDSTF 432

Query: 413 WHSGVTGLIDIVYNKGHSTVIILDNSITAMTGHQENPSTGKTLSGERTNQIDFEALGRSI 472
            H G+ GL+DIVYN+G+ TV+ILDN  T MTG Q +  TGK L G+ T ++DF  L  ++
Sbjct: 433 LHMGMQGLLDIVYNRGNVTVLILDNRTTGMTGGQNHAGTGKGLKGDDTPRVDFAKLVEAL 492

Query: 473 GI--NRICVVDAYDLKALEETIKEEVNAEEPSLIITKRPCVLIKGAKFDFKDYKIDPKLC 530
           G+   RI  +D Y L  + +TIK+E    E S+IIT RPCVL +      + YK+  + C
Sbjct: 493 GVKPERISKIDPYVLPVVFKTIKQETAIPEVSVIITDRPCVLSE-FYTKIEPYKVIDEDC 551

Query: 531 TGCKLCLKAGCPAISF---------DGKV-----AKINDSLCVGCGLCKDLCKFSAIV 574
           TGC  C+  GCPAI+          DGKV       I+ ++C GC +C + C   AIV
Sbjct: 552 TGCGNCINVGCPAITVKRSESKVRPDGKVNELKFTTIDTAMCTGCHMCVESCGPKAIV 609


Lambda     K      H
   0.317    0.136    0.392 

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: 871
Number of extensions: 42
Number of successful extensions: 11
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: 578
Length of database: 618
Length adjustment: 37
Effective length of query: 541
Effective length of database: 581
Effective search space:   314321
Effective search space used:   314321
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: 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