GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fecD in Caldicellulosiruptor hydrothermalis 108

Align iron(III) dicitrate transport system permease protein FecD (characterized)
to candidate WP_013402813.1 CALHY_RS04480 iron ABC transporter permease

Query= CharProtDB::CH_004160
         (318 letters)



>NCBI__GCF_000166355.1:WP_013402813.1
          Length = 336

 Score =  199 bits (505), Expect = 1e-55
 Identities = 114/325 (35%), Positives = 196/325 (60%), Gaps = 16/325 (4%)

Query: 5   LVIFITLALAGCALLSLHMGVIPVP----WRALLT-----DWQAGHEHYYVLMEYRLPRL 55
           ++I + L L    ++S+ +G + +P     +ALL+        A      ++ + RLPR+
Sbjct: 4   VLIILALLLLTVFIISIGVGSVFIPPLRVLKALLSLIGISFGPANDMDLTIVGQIRLPRI 63

Query: 56  LLALFVGAALAVAGVLIQGIVRNPLASPDILGVNHAASLASVGALLL-MPSLPVMVLPLL 114
           ++A+ VG +L++AG L+QG+ RNP+A P I+G +  ASL ++  +   + ++ +  LPLL
Sbjct: 64  IIAMIVGMSLSIAGALVQGLYRNPMADPGIIGTSSGASLGAIVCIAFSLNTINIFYLPLL 123

Query: 115 AFAGGMAGLILLKMLAKTHQPM---KLALTGVALSACWASLTDYLMLSRPQ-DVNNALLW 170
           AFAG +    L+  L+  +       L L G+A+S   +S+   ++ +  Q  V+  + W
Sbjct: 124 AFAGALLISFLVYRLSTKNNKTPITNLILIGIAVSTFVSSINSLILSNINQYQVSEYIFW 183

Query: 171 LTGSLWGRDWSFVKIA-IPLMILFLPLSLSFCRDLDLLALGDARATTLGVSVPHTRFWAL 229
           + GSL GR W  VKI+ +PL IL L  SL F + +++L LG+  + T+GV+    +   L
Sbjct: 184 MLGSLDGRSWVHVKISFVPLCILIL-CSLLFAKRINILILGEEESFTIGVNPEKLKKTLL 242

Query: 230 LLAVAMTSTGVAACGPISFIGLVVPHMMRSITGGRHRRLLPVSALTGALLLVVADLLARI 289
            L   +T   V+  GPISF+GL+VPHM+R I G  +RRL+P S L+G + L++ D +AR+
Sbjct: 243 FLVSLITGIAVSVSGPISFVGLIVPHMLRLIVGSDYRRLIPASILSGGIFLIMCDTIARV 302

Query: 290 IHPPLELPVGVLTAIIGAPWFVWLL 314
           +  P+E+ VG++T+++G P+F++LL
Sbjct: 303 LFSPVEVKVGIITSLVGVPYFLYLL 327


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: 244
Number of extensions: 8
Number of successful extensions: 2
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: 336
Length adjustment: 28
Effective length of query: 290
Effective length of database: 308
Effective search space:    89320
Effective search space used:    89320
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: 48 (23.1 bits)

This GapMind analysis is from Sep 24 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