GapMind for catabolism of small carbon sources

 

Aligments for a candidate for livG in Caulobacter crescentus NA1000

Align High-affinity branched-chain amino acid transport ATP-binding protein BraF, component of Branched chain amino acid uptake transporter. Transports alanine (characterized)
to candidate CCNA_03235 CCNA_03235 spermidine/putrescine transport ATP-binding protein potA

Query= TCDB::P21629
         (255 letters)



>lcl|FitnessBrowser__Caulo:CCNA_03235 CCNA_03235
           spermidine/putrescine transport ATP-binding protein potA
          Length = 381

 Score =  130 bits (327), Expect = 4e-35
 Identities = 75/244 (30%), Positives = 129/244 (52%), Gaps = 18/244 (7%)

Query: 3   RPILEVSGLTMRFGGLLAVNGVNLKVEEKQVVSMIGPNGAGKTTVFNCLTGFYQPTGGLI 62
           +PI+    +T RFG L AV+ V+L V E +  +++GP+G GKTT+   L GF  PT G I
Sbjct: 12  KPIITFENVTKRFGKLAAVDNVSLTVNEGEFFALLGPSGCGKTTLLRMLAGFETPTEGRI 71

Query: 63  RLDGEEIQGLPGHKIARKGVVRTFQNVRLFKEMTAVENLLVAQHRHLNTNFLAGLFKTPA 122
            +DG++I  +P +K   + V   FQ+  +F  MT  +N+                 K   
Sbjct: 72  LIDGQDISNVPPNK---RPVNMVFQSYAVFPHMTVADNVAYG-------------LKVDN 115

Query: 123 FRRSEREAMEYAAHWLEEVNLTEFANRSAGTLAYGQQRRLEIARCMMTRPRILMLDEPAA 182
             ++EREA    A  LE V L     R    L+ GQ++R+ +AR ++ RPR+L+LDEP +
Sbjct: 116 VPKAEREAR--VAEALELVQLGGLGGRKPDQLSGGQRQRVALARALVKRPRVLLLDEPLS 173

Query: 183 GLNPKETDDLKALIAKLRSEHNVTVLLIEHDMKLVMSISDHIVVINQGAPLADGTPEQIR 242
            L+ K  + ++  +  L+ +  +T +++ HD    ++++    V+++G      TP  + 
Sbjct: 174 ALDAKLREQMRTELCTLQEKVGITFIMVTHDQDEALALASRCAVMSKGLLQQVATPSDLY 233

Query: 243 DNPD 246
           + P+
Sbjct: 234 EFPN 237


Lambda     K      H
   0.320    0.137    0.391 

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: 237
Number of extensions: 10
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: 255
Length of database: 381
Length adjustment: 27
Effective length of query: 228
Effective length of database: 354
Effective search space:    80712
Effective search space used:    80712
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 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