GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__Caulo:CCNA_03238 CCNA_03238 ABC-type
           spermidine/putrescine transport system, permease
           component II
          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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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