GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lutB in Pseudomonas fluorescens FW300-N2E2

Align Iron-sulfur cluster binding protein (characterized, see rationale)
to candidate Pf6N2E2_3383 Predicted L-lactate dehydrogenase, Iron-sulfur cluster-binding subunit YkgF

Query= uniprot:E4PLR6
         (483 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3383
          Length = 242

 Score =  397 bits (1020), Expect = e-115
 Identities = 189/241 (78%), Positives = 207/241 (85%), Gaps = 1/241 (0%)

Query: 242 VTGIEKVVPNLRDVVPLVSLLTRSALGQPITTYVNLISGPRKPDELDGPEEVHLVLLDNG 301
           VTGIEKVV NLRDVVPL+SLLTRSALGQPITTYVN+ISGPRK DELDGP+EVHLVLLDNG
Sbjct: 1   VTGIEKVVENLRDVVPLLSLLTRSALGQPITTYVNMISGPRKADELDGPQEVHLVLLDNG 60

Query: 302 RTGAFADAQMRQTLNCIRCGACMNHCPVYTRVGGHTYGEVYPGPIGKIITPHMAGLDKVP 361
           R+ AFAD+++RQTLNCIRCGACMNHCPVYTR+GGH YGEVYPGPIGKIITPHM GL KVP
Sbjct: 61  RSQAFADSELRQTLNCIRCGACMNHCPVYTRIGGHAYGEVYPGPIGKIITPHMVGLAKVP 120

Query: 362 DHPSASSLCGACGEVCPVKIPIPELLQRLRQENVKNPEQPQQV-KGGGAKYSRTERWIWR 420
           DHPSASSLCGACGEVCPVKIPIP LL+RLR+ENVK P+ P QV +G G+KYS  ER+IW 
Sbjct: 121 DHPSASSLCGACGEVCPVKIPIPALLRRLREENVKAPDSPHQVMRGQGSKYSPKERFIWN 180

Query: 421 GWQMLNTRPALYRSFLWAATRFRALAPKKAGPWTENHSAPVPARRSLHDLAARHLDQNGG 480
            W  LN+ P LYR F + ATR RAL P   GPWT+NHSAP PA RSLHDLA  HL+Q G 
Sbjct: 181 AWARLNSSPRLYRLFGFLATRLRALTPNNVGPWTQNHSAPKPAARSLHDLARDHLNQQGD 240

Query: 481 R 481
           R
Sbjct: 241 R 241


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: 385
Number of extensions: 16
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: 242
Length adjustment: 28
Effective length of query: 455
Effective length of database: 214
Effective search space:    97370
Effective search space used:    97370
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: 49 (23.5 bits)

Align Iron-sulfur cluster binding protein (characterized, see rationale)
to candidate Pf6N2E2_3382 Predicted L-lactate dehydrogenase, Iron-sulfur cluster-binding subunit YkgF

Query= uniprot:E4PLR6
         (483 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3382
          Length = 187

 Score =  191 bits (484), Expect = 2e-53
 Identities = 103/177 (58%), Positives = 118/177 (66%), Gaps = 17/177 (9%)

Query: 5   IPVTELTPDFRGRAEEALADGQLRNNFRVAMDSLMTKRANAFPDADEREGLRELGNRIKA 64
           IP  E+  DFR RA +AL D QLRNNFR AMDSLMTKRA +F DA ERE LR LGN ++A
Sbjct: 7   IPTVEVQEDFRARAHKALDDTQLRNNFRSAMDSLMTKRATSFSDAHEREHLRVLGNAVRA 66

Query: 65  GALSRLPDLLEQLEQKLTENGVKVHWAETVEEANSLVHGIIEARKGSQVVKGKSMVSEEM 124
            ALS+LPDLLEQLE  LT NGV VHWAETV+EAN +V  II A +  QV+KGKSMVSEEM
Sbjct: 67  RALSKLPDLLEQLETNLTRNGVNVHWAETVDEANGIVLSIIRAHEARQVIKGKSMVSEEM 126

Query: 125 EMNDYLAERGVECLESDMGEYIVQLDNEKPSHIIMPAIHKNARQVSKLFHDKLGEPE 181
           EMN +L  R +ECLESDMG                  IH+ AR      H   G+P+
Sbjct: 127 EMNHFLEARDIECLESDMG-----------------GIHRPARPREAFTHHYAGDPQ 166


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: 241
Number of extensions: 10
Number of successful extensions: 1
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: 187
Length adjustment: 26
Effective length of query: 457
Effective length of database: 161
Effective search space:    73577
Effective search space used:    73577
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: 48 (23.1 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