GapMind for catabolism of small carbon sources

 

Alignments for a candidate for potB in Caulobacter crescentus NA1000

Align putrescine transport system permease protein PotH (characterized)
to candidate CCNA_03238 CCNA_03238 ABC-type spermidine/putrescine transport system, permease component II

Query= CharProtDB::CH_088338
         (317 letters)



>FitnessBrowser__Caulo:CCNA_03238
          Length = 306

 Score =  205 bits (522), Expect = 1e-57
 Identities = 109/282 (38%), Positives = 168/282 (59%), Gaps = 28/282 (9%)

Query: 36  PYIWLILLFLLPFLIVFKISLAEMARAIPPYTELMEWADGQLSITLNLGNFLQLTDDPLY 95
           P +WL+L FL P  IV+  S                    +++I+    N+ +  + PLY
Sbjct: 23  PLVWLVLFFLAPMAIVWAYSFGHNVGLT------------EIAISGTFHNYARAIE-PLY 69

Query: 96  FDAYLQSLQVAAISTFCCLLIGYPLAWAVAHSKPSTRNILLLLVILPSWTSFLIRVYAWM 155
              +L+S+ VA ++T  CL+IG+P+A A+  +    +  LLLL++LP WT+ LIR YA +
Sbjct: 70  LKIFLKSVWVAGLTTGLCLVIGFPVALAITFASDKAKAWLLLLIMLPFWTNLLIRTYALI 129

Query: 156 GILKNNGVLNNFLLWL-----GVID----------QPLTILHTNLAVYIGIVYAYVPFMV 200
            +L+  G +N  L W      G+            QPL +LH N AV +G+VY ++PFMV
Sbjct: 130 AVLRTEGYVNQGLEWFWKGGSGLATLIGLQPLGDFQPLELLHNNFAVILGLVYVHLPFMV 189

Query: 201 LPIYTALIRIDYSLVEAALDLGARPLKTFFTVIVPLTKGGIIAGSMLVFIPAVGEFVIPE 260
           LP+Y+AL R+D SL+EA+LDLGA  L+T F V+VPL   GI +G ++ FIPA+G ++ P+
Sbjct: 190 LPLYSALDRLDKSLLEASLDLGAGHLRTLFKVVVPLAIPGIASGVLITFIPALGAYLTPD 249

Query: 261 LLGGPDSIMIGRVLWQEFFNNRDWPVASAVAIIMLLLLIVPI 302
           LLGGPDS MI  ++ ++F    DWP  +A++ +++ L  + I
Sbjct: 250 LLGGPDSQMIANIIERQFKRANDWPFGAALSFLLMYLTFIAI 291


Lambda     K      H
   0.328    0.144    0.457 

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: 299
Number of extensions: 17
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: 317
Length of database: 306
Length adjustment: 27
Effective length of query: 290
Effective length of database: 279
Effective search space:    80910
Effective search space used:    80910
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 (21.7 bits)
S2: 48 (23.1 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