GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fecD in Nocardiopsis lucentensis DSM 44048

Align iron(III) dicitrate transport system permease protein FecD (characterized)
to candidate WP_241479666.1 D471_RS0120295 iron ABC transporter permease

Query= CharProtDB::CH_004160
         (318 letters)



>NCBI__GCF_000341125.1:WP_241479666.1
          Length = 341

 Score =  191 bits (485), Expect = 2e-53
 Identities = 130/332 (39%), Positives = 185/332 (55%), Gaps = 21/332 (6%)

Query: 5   LVIFITLALAGCALLSLHMGVIPVP--------WRALLTDWQAGHEHY--YVLMEYRLPR 54
           L+  +T AL   AL+S  +G  PVP          A+  D     +     VL + RLPR
Sbjct: 6   LLTGLTAALVAVALVSAGLGAYPVPVDQVAASLLHAIGLDLGTPPDRIGQTVLWDVRLPR 65

Query: 55  LLLALFVGAALAVAGVLIQGIVRNPLASPDILGVNHAASLASVGALLLMPSLPVM---VL 111
           + LA+ VGAAL VAG ++QGI  NPLA P ++GV+  A++ ++  L++   L V     +
Sbjct: 66  VTLAVAVGAALGVAGAMMQGIFGNPLAEPGVIGVSSGAAVGAI--LVIFSGLTVFGHWTI 123

Query: 112 PLLAFAGGMAGLILLKMLAKTH---QPMKLALTGVALSACWASLTDYLMLSRPQD--VNN 166
              +F  G+A  + + + A++H   + + L LTGVA++A  A     LM +  QD  +  
Sbjct: 124 IASSFVFGLATTLFVYVFARSHGRTEVVTLLLTGVAVNAV-AGAAIGLMTNFSQDAQIQT 182

Query: 167 ALLWLTGSLWGRDWSFVKIAIPLMILFLPLSLSFCRDLDLLALGDARATTLGVSVPHTRF 226
              W  GS+    W+ V    P ++L L +   + R LDLLALG+  A  LGV V   R 
Sbjct: 183 ITFWQLGSVSTATWAKVAAITPCLLLGLAVIPLYARRLDLLALGEGPARHLGVDVERMRL 242

Query: 227 WALLLAVAMTSTGVAACGPISFIGLVVPHMMRSITGGRHRRLLPVSALTGALLLVVADLL 286
             +     +TS  VA  G ++FIGLVVPH++R +TG  HR LLP SAL G LLL+ ADLL
Sbjct: 243 VVIAALALLTSAAVAFAGIVAFIGLVVPHIVRMVTGPGHRILLPSSALGGGLLLMSADLL 302

Query: 287 ARIIHPPLELPVGVLTAIIGAPWFVWLLVRMR 318
           AR    P E+P+GV+TA +G P+F +LL R R
Sbjct: 303 ARTAAAPAEIPLGVVTAALGGPFFFFLLHRTR 334


Lambda     K      H
   0.330    0.142    0.447 

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: 278
Number of extensions: 12
Number of successful extensions: 3
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: 318
Length of database: 341
Length adjustment: 28
Effective length of query: 290
Effective length of database: 313
Effective search space:    90770
Effective search space used:    90770
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 49 (23.5 bits)

This GapMind analysis is from Apr 09 2024. 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