GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lldF in Pseudomonas fluorescens FW300-N2C3

Align 4Fe-4S ferredoxin-type domain-containing protein (characterized, see rationale)
to candidate AO356_07560 AO356_07560 (Fe-S)-binding protein

Query= uniprot:B2TBY8
         (464 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_07560
          Length = 489

 Score =  276 bits (706), Expect = 1e-78
 Identities = 170/444 (38%), Positives = 235/444 (52%), Gaps = 36/444 (8%)

Query: 31  LREKRDAQAHGIAEWETMRELASGIKEHTLSNLSQYLEQFAAAAEANGVTVHWAATAEEH 90
           L  KR A      E E +R L + ++   LS L   LEQ       NGV VHWA T +E 
Sbjct: 44  LMTKRAASFSDAHEREHLRVLGNAVRARALSKLPDLLEQLETNLTRNGVNVHWAETVDEA 103

Query: 91  NALVHQIMSERGMTTLVKSKSMLTDECKMREYLEPRGITVMETDLGERIQQLDHQDPSHM 150
           N +V  I+       ++K KSM+++E +M  +LE R I  +E+D+GE I QLDH+ PSH+
Sbjct: 104 NGIVLSIIRAHEARQVIKGKSMVSEEMEMNHFLEARDIECLESDMGEYIVQLDHEKPSHI 163

Query: 151 VVPAVHKLRADVAELFGRTIGTDPKNSDIHYLAESQRMNTRPYFVREKTAGMTGCNFAVA 210
           ++PA+HK    VA LF   +G +    D+  L +  R   R  F  E   G++G NFAVA
Sbjct: 164 IMPAIHKNAGQVASLFHDKLGVE-YTKDVDQLIQIGRKVLRQKFF-EADIGVSGVNFAVA 221

Query: 211 ETGTVVVCTNEGNADLSANVPPLHIASIGIEKLIPKVSDLGVFIRMLSRSALGSPITQYT 270
           ETGT+++  NEGN  +S  VPP+HIA  GIEK++  + D+   + +L+RSALG PIT Y 
Sbjct: 222 ETGTLLLVENEGNGRMSTTVPPVHIAVTGIEKVVENLRDVVPLLSLLTRSALGQPITTYV 281

Query: 271 SHFRAPRPGTEM------HFILVDHGRSERLAMEDFWYSLKCIRCGACMNTCPVYRRSGG 324
           +    PR   E+      H +L+D+GRS+  A  +   +L CIRCGACMN CPVY R GG
Sbjct: 282 NMISGPRKADELDGPQEVHLVLLDNGRSQAFADSELRQTLNCIRCGACMNHCPVYTRIGG 341

Query: 325 LSYGGTYSGPIGAIINP-TFDLKRYSALPFASTLNGSCTNVCPVKINIHEQIYKWRTVIA 383
            +YG  Y GPIG II P    L +    P AS+L G+C  VCPVKI I   + + R    
Sbjct: 342 HAYGEVYPGPIGKIITPHMVGLAKVPDHPSASSLCGACGEVCPVKIPIPALLRRLR---E 398

Query: 384 ERHEVPFVKQEVLKMAGR---------------LLASPTLYRATVSSMGSALRRLPNFVL 428
           E  + P    +V++  G                L +SP LYR     + + LR L     
Sbjct: 399 ENVKAPDSPNQVMRGQGSKYSPKERFIWNAWAWLNSSPRLYR-LFGFLATRLRAL----- 452

Query: 429 YNPLNI--WGKQRELPEAPKLTFH 450
             P N+  W +    P+    + H
Sbjct: 453 -TPKNLGPWTQNHSAPQPAARSLH 475


Lambda     K      H
   0.320    0.133    0.406 

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: 490
Number of extensions: 26
Number of successful extensions: 6
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: 464
Length of database: 489
Length adjustment: 33
Effective length of query: 431
Effective length of database: 456
Effective search space:   196536
Effective search space used:   196536
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 51 (24.3 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