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

GapMind for catabolism of small carbon sources

Aligments 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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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

GapMind for catabolism of small carbon sources