GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lutB in Pseudomonas fluorescens GW456-L13

Align Iron-sulfur cluster binding protein (characterized, see rationale)
to candidate PfGW456L13_5116 Predicted L-lactate dehydrogenase, Iron-sulfur cluster-binding subunit YkgF

Query= uniprot:E4PLR6
         (483 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_5116
          Length = 485

 Score =  743 bits (1918), Expect = 0.0
 Identities = 368/478 (76%), Positives = 405/478 (84%), Gaps = 1/478 (0%)

Query: 5   IPVTELTPDFRGRAEEALADGQLRNNFRVAMDSLMTKRANAFPDADEREGLRELGNRIKA 64
           IP   +  DFR RA  AL D QLR+NFR AMDSLMTKRA AF DA ERE LR LGN I+A
Sbjct: 7   IPTVAVEEDFRTRAHNALGDPQLRSNFRKAMDSLMTKRAAAFSDAHEREHLRALGNAIRA 66

Query: 65  GALSRLPDLLEQLEQKLTENGVKVHWAETVEEANSLVHGIIEARKGSQVVKGKSMVSEEM 124
            ALS+LPDLLEQLEQ LT NGV VHWAETV+EAN +V  II A +G QV+KGKSMVSEEM
Sbjct: 67  RALSKLPDLLEQLEQNLTRNGVTVHWAETVDEANGIVLSIIRAHEGRQVIKGKSMVSEEM 126

Query: 125 EMNDYLAERGVECLESDMGEYIVQLDNEKPSHIIMPAIHKNARQVSKLFHDKLGEPETED 184
           EMN  LAE+G+ECLESDMGEYIVQLD+EKPSHIIMPAIHKNA QV+ LFHDKLG   T+D
Sbjct: 127 EMNHVLAEQGIECLESDMGEYIVQLDHEKPSHIIMPAIHKNAGQVASLFHDKLGVEYTKD 186

Query: 185 VNQLIQIGRRTLRRKFMEADVGVSGVNFAIAETGTLLLVENEGNGRMSTTAPPVHIAVTG 244
           V+QLIQIGRR LR+KF EAD+GVSGVNFA+AETGTLLLVENEGNGRM+TT PPVHIAVTG
Sbjct: 187 VDQLIQIGRRVLRQKFFEADIGVSGVNFAVAETGTLLLVENEGNGRMTTTVPPVHIAVTG 246

Query: 245 IEKVVPNLRDVVPLVSLLTRSALGQPITTYVNLISGPRKPDELDGPEEVHLVLLDNGRTG 304
           IEKVV NLRDVVPL+SLLTRSALG PITTYVN+ISGPRK  ELDGP+EVHLVLLDNGR+ 
Sbjct: 247 IEKVVENLRDVVPLLSLLTRSALGIPITTYVNMISGPRKEHELDGPQEVHLVLLDNGRSQ 306

Query: 305 AFADAQMRQTLNCIRCGACMNHCPVYTRVGGHTYGEVYPGPIGKIITPHMAGLDKVPDHP 364
           AFAD+++RQTLNCIRCGACMNHCPVYTR+GGH YGEVYPGPIGKIITPHM GL KVPDHP
Sbjct: 307 AFADSELRQTLNCIRCGACMNHCPVYTRIGGHAYGEVYPGPIGKIITPHMVGLAKVPDHP 366

Query: 365 SASSLCGACGEVCPVKIPIPELLQRLRQENVKNPEQPQQV-KGGGAKYSRTERWIWRGWQ 423
           SASSLCGACGEVCPVKIPIP LL+RLR+ENVK P+ P QV +G G+KYSR ER+IW  W 
Sbjct: 367 SASSLCGACGEVCPVKIPIPALLRRLREENVKAPDSPHQVMRGQGSKYSRKERFIWNAWA 426

Query: 424 MLNTRPALYRSFLWAATRFRALAPKKAGPWTENHSAPVPARRSLHDLAARHLDQNGGR 481
            LN+ P LYR F + ATR RAL P   GPWT+NHSAP PA RSLHD+A  HL + G R
Sbjct: 427 KLNSSPTLYRLFGFFATRLRALTPSNVGPWTQNHSAPKPAARSLHDMAREHLAKQGER 484


Lambda     K      H
   0.317    0.135    0.403 

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: 741
Number of extensions: 29
Number of successful extensions: 4
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: 483
Length of database: 485
Length adjustment: 34
Effective length of query: 449
Effective length of database: 451
Effective search space:   202499
Effective search space used:   202499
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: 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