GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lldF in Pseudomonas stutzeri RCH2

Align 4Fe-4S ferredoxin-type domain-containing protein (characterized, see rationale)
to candidate GFF924 Psest_0953 iron-sulfur cluster-binding protein

Query= uniprot:B2TBY8
         (464 letters)



>FitnessBrowser__psRCH2:GFF924
          Length = 486

 Score =  283 bits (725), Expect = 7e-81
 Identities = 176/441 (39%), Positives = 240/441 (54%), Gaps = 30/441 (6%)

Query: 31  LREKRDAQAHGIAEWETMRELASGIKEHTLSNLSQYLEQFAAAAEANGVTVHWAATAEEH 90
           L  KR        E E +RE+ + I+   LS L + LE+       NGV VHWA T EE 
Sbjct: 44  LMTKRAVAFSDADERERLREMGNRIRARALSKLPELLERLETNLTRNGVNVHWAETVEEA 103

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

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

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

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

Query: 325 LSYGGTYSGPIGAIINP-TFDLKRYSALPFASTLNGSCTNVCPVKINIHEQIYKWRTVIA 383
            +YG  Y GPIG II P    L +    P AS+L G+C  VCPVKI I   + + R    
Sbjct: 342 HTYGEVYPGPIGKIITPHMVGLDKVPDHPSASSLCGACGEVCPVKIPIPSILRRLREENI 401

Query: 384 ERHEVP----------FVKQEVLKMAG-RLL-ASPTLYRATVSSMGSALRRLPNFVLYNP 431
           +  + P          + K+E L  AG RLL  +PTLYR       + LR L       P
Sbjct: 402 KAPDDPHKVMRGQGSKYSKKERLMWAGWRLLNTNPTLYR-VFGFFATRLRGL------TP 454

Query: 432 LNI--WGKQRELPEAPKLTFH 450
            NI  W +    P+    + H
Sbjct: 455 SNIGPWTQNHSAPKPAARSLH 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: 525
Number of extensions: 27
Number of successful extensions: 5
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: 486
Length adjustment: 33
Effective length of query: 431
Effective length of database: 453
Effective search space:   195243
Effective search space used:   195243
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