GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mtlK in Caulobacter crescentus NA1000

Align ABC transporter for D-Sorbitol, ATPase component (characterized)
to candidate CCNA_03235 CCNA_03235 spermidine/putrescine transport ATP-binding protein potA

Query= reanno::acidovorax_3H11:Ac3H11_2941
         (350 letters)



>FitnessBrowser__Caulo:CCNA_03235
          Length = 381

 Score =  231 bits (588), Expect = 3e-65
 Identities = 138/356 (38%), Positives = 196/356 (55%), Gaps = 32/356 (8%)

Query: 4   LQLRGIEKFFGEHRAIKGIDLTIQQGEFIVFVGPSGCGKSTLLRLIAGLEAIDGGSLMLD 63
           +    + K FG+  A+  + LT+ +GEF   +GPSGCGK+TLLR++AG E    G +++D
Sbjct: 15  ITFENVTKRFGKLAAVDNVSLTVNEGEFFALLGPSGCGKTTLLRMLAGFETPTEGRILID 74

Query: 64  GRDITDQPSSKRDLAMVFQSYALYPHMSVYENMSFALKLAKVDKQVIDEKVQNAARILNL 123
           G+DI++ P +KR + MVFQSYA++PHM+V +N+++ LK+  V K   + +V  A  ++ L
Sbjct: 75  GQDISNVPPNKRPVNMVFQSYAVFPHMTVADNVAYGLKVDNVPKAEREARVAEALELVQL 134

Query: 124 TQYLQRTPKELSGGQRQRVAIGRAIVRAPKVFLFDEPLSNLDAALRGQTRVEIAKLHRDL 183
                R P +LSGGQRQRVA+ RA+V+ P+V L DEPLS LDA LR Q R E+  L   +
Sbjct: 135 GGLGGRKPDQLSGGQRQRVALARALVKRPRVLLLDEPLSALDAKLREQMRTELCTLQEKV 194

Query: 184 GATTIYVTHDQVEAMTLADRVVVLRDGIIEQVGTPLELYDKPANQFVAQFIG-------- 235
           G T I VTHDQ EA+ LA R  V+  G+++QV TP +LY+ P ++FVA FIG        
Sbjct: 195 GITFIMVTHDQDEALALASRCAVMSKGLLQQVATPSDLYEFPNSRFVADFIGQVNLFEGV 254

Query: 236 ----TPQMNVVPVDKLPQPV-QQQAPAAPAGAAVGAIGLRPENITVR------------- 277
                P   V+    LP  +        P G  V A  +RPE I +              
Sbjct: 255 LAVDEPSHAVIKSPDLPVDIFLDHGVTGPRGGTVWA-AIRPEKIELHKKADDTPPNLGDA 313

Query: 278 TTGATPVGGQVDLIEALGAETLIYVTTPGGAQF-VSRQN----DRTDLRVGDAVSL 328
             G   V G +     LG  +   V   GG +  V R N    D+ D ++G+ V L
Sbjct: 314 PKGTNAVEGVIKHEAYLGGSSTYEVEIAGGRRVKVQRSNLTRWDQEDFKLGETVWL 369


Lambda     K      H
   0.320    0.137    0.388 

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: 333
Number of extensions: 10
Number of successful extensions: 1
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: 350
Length of database: 381
Length adjustment: 30
Effective length of query: 320
Effective length of database: 351
Effective search space:   112320
Effective search space used:   112320
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: 49 (23.5 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