GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lldF in Cupriavidus basilensis 4G11

Align 4Fe-4S ferredoxin-type domain-containing protein (characterized, see rationale)
to candidate RR42_RS21285 RR42_RS21285 (Fe-S)-binding protein

Query= uniprot:B2TBY8
         (464 letters)



>FitnessBrowser__Cup4G11:RR42_RS21285
          Length = 476

 Score =  278 bits (712), Expect = 2e-79
 Identities = 155/357 (43%), Positives = 213/357 (59%), Gaps = 8/357 (2%)

Query: 31  LREKRDAQAHGIAEWETMRELASGIKEHTLSNLSQYLEQFAAAAEANGVTVHWAATAEEH 90
           L+ KR  Q     E E +R+L   I++H LS L   L Q      A GV VHWA TA+E 
Sbjct: 33  LQAKRAVQFPDGDELEQLRDLGEAIRQHALSQLPDLLVQLEDKLTAAGVQVHWAETADEA 92

Query: 91  NALVHQIMSERGMTTLVKSKSMLTDECKMREYLEPRGITVMETDLGERIQQLDHQDPSHM 150
           NA+VH I   R  + ++K KSM ++E ++  YL  RGI  +E+D+GE I QL  + PSH+
Sbjct: 93  NAIVHGIAQARQASRVIKGKSMASEEIELNHYLAERGIDCIESDMGEYIVQLAGEKPSHI 152

Query: 151 VVPAVHKLRADVAELFGRTIGTDPKNSDIHYLAESQRMNTRPYFVREKTAGMTGCNFAVA 210
           V+PA+HK R D+AELF + I   P   D+  L ++ R   R  FV     G++G NFA A
Sbjct: 153 VMPAIHKTRGDIAELFEQHIPGTPYTEDVDELIQTGRRALRQEFV-NADIGLSGVNFAAA 211

Query: 211 ETGTVVVCTNEGNADLSANVPPLHIASIGIEKLIPKVSDLGVFIRMLSRSALGSPITQYT 270
           +TGT+ +  NEGN  LS  VP +HIA +G+EK++ ++  +     +L+RSA G  IT Y 
Sbjct: 212 DTGTLWLVENEGNGRLSTTVPDVHIAIMGMEKVVARLEHIVPLASLLTRSATGQAITTYF 271

Query: 271 SHFRAPRPG------TEMHFILVDHGRSERLAMEDFWYSLKCIRCGACMNTCPVYRRSGG 324
           +    PR         E+H +L+D+GRS+  A E    +L+CIRCGACMN CPVY R GG
Sbjct: 272 NLISGPRRAGERDGPREVHLVLLDNGRSQAYADEQLRATLQCIRCGACMNHCPVYTRIGG 331

Query: 325 LSYGGTYSGPIGAIINP-TFDLKRYSALPFASTLNGSCTNVCPVKINIHEQIYKWRT 380
            +YG TY GPIG II+P    L   + L  AS+L G+C  VCPV+I I + + + RT
Sbjct: 332 HAYGTTYPGPIGKIISPHLLGLDATADLATASSLCGACGEVCPVRIPIPQLLIRLRT 388


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: 499
Number of extensions: 25
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: 476
Length adjustment: 33
Effective length of query: 431
Effective length of database: 443
Effective search space:   190933
Effective search space used:   190933
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