GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lutB in Marinobacter adhaerens HP15

Align Iron-sulfur cluster binding protein (characterized, see rationale)
to candidate GFF2943 HP15_2887 iron-sulfur cluster binding protein

Query= uniprot:E4PLR6
         (483 letters)



>FitnessBrowser__Marino:GFF2943
          Length = 479

 Score =  570 bits (1468), Expect = e-167
 Identities = 286/457 (62%), Positives = 343/457 (75%), Gaps = 2/457 (0%)

Query: 13  DFRGRAEEALADGQLRNNFRVAMDSLMTKRANAFPDADEREGLRELGNRIKAGALSRLPD 72
           +F  RA+ A+ D ++R NFR AMD LM+KR  AF   D  E LR+LG  ++  AL+ LPD
Sbjct: 16  EFHPRAQAAIHDPKIRKNFRSAMDGLMSKRKTAFEGWD-LETLRDLGANVRLRALANLPD 74

Query: 73  LLEQLEQKLTENGVKVHWAETVEEANSLVHGIIEARKGSQVVKGKSMVSEEMEMNDYLAE 132
           LLEQLE+KL ENG+KVHWA   +EA  +V  I +AR    V+KGKSMVSEEME+N YL E
Sbjct: 75  LLEQLEKKLIENGIKVHWAVDGDEACRIVRDICKARDAKTVIKGKSMVSEEMELNHYLEE 134

Query: 133 RGVECLESDMGEYIVQLDNEKPSHIIMPAIHKNARQVSKLFHDKLGEPETEDVNQLIQIG 192
           +G+E LESD+GEYIVQL +E PSHIIMPAIHKN  ++S+L H+K G   + DV  L    
Sbjct: 135 QGIEALESDLGEYIVQLADETPSHIIMPAIHKNTGEISQLLHEKTGTDLSNDVEYLTASA 194

Query: 193 RRTLRRKFMEADVGVSGVNFAIAETGTLLLVENEGNGRMSTTAPPVHIAVTGIEKVVPNL 252
           R  LR KFM ADVGVSGVNFA+AETGTL LVENEGNGRM+TT P  HIAVTGIEKVVP++
Sbjct: 195 RLQLREKFMNADVGVSGVNFAVAETGTLCLVENEGNGRMTTTVPKCHIAVTGIEKVVPSM 254

Query: 253 RDVVPLVSLLTRSALGQPITTYVNLISGPRKPDELDGPEEVHLVLLDNGRTGAFADAQMR 312
            DV  L++LLTRSA GQ ITTY N+ISGPRK +ELDGPEEVHLVL+DNGR+  + D ++ 
Sbjct: 255 EDVSALLALLTRSATGQHITTYFNMISGPRKAEELDGPEEVHLVLVDNGRSSIYQDDELL 314

Query: 313 QTLNCIRCGACMNHCPVYTRVGGHTYGEVYPGPIGKIITPHMAGLDKVPDHPSASSLCGA 372
            TL CIRCGACMNHCPVYTRVGGH YG  YPGPIGKI+ PH+ GLD+    PSASSLCGA
Sbjct: 315 DTLRCIRCGACMNHCPVYTRVGGHAYGTTYPGPIGKILMPHLIGLDEGRHLPSASSLCGA 374

Query: 373 CGEVCPVKIPIPELLQRLRQENVKNPE-QPQQVKGGGAKYSRTERWIWRGWQMLNTRPAL 431
           CGEVCPVKIPIP+LL RLRQE+V   +  P +V+G GAK S  E  IW+GW  ++  P +
Sbjct: 375 CGEVCPVKIPIPDLLVRLRQESVDGDKLHPAKVRGHGAKRSSMEAMIWKGWAWMHASPGI 434

Query: 432 YRSFLWAATRFRALAPKKAGPWTENHSAPVPARRSLH 468
           YR    AA++FRAL P KAG WT+  +AP  A ++LH
Sbjct: 435 YRFGTGAASKFRALQPSKAGAWTDYRTAPKLAAKTLH 471


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: 682
Number of extensions: 23
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: 483
Length of database: 479
Length adjustment: 34
Effective length of query: 449
Effective length of database: 445
Effective search space:   199805
Effective search space used:   199805
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: 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