GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Ac3H11_1693 in Alkalihalobacterium alkalinitrilicum DSM 22532

Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate WP_078427103.1 BK574_RS00955 ABC transporter ATP-binding protein

Query= uniprot:A0A165KC86
         (260 letters)



>NCBI__GCF_002019605.1:WP_078427103.1
          Length = 509

 Score =  125 bits (314), Expect = 2e-33
 Identities = 69/228 (30%), Positives = 122/228 (53%), Gaps = 12/228 (5%)

Query: 9   VLKVAGISKRFGGLQALSDVGITIKRGQVYGLIGPNGAGKTTFFNVITGLYTPDAGTFEL 68
           V+++  I K F G+ A  +V + +K+G+++ L+G NGAGK+T  NV+ GLY P+ G   +
Sbjct: 4   VIEMKDIRKEFPGIVANDNVTLQVKQGEIHALLGENGAGKSTLMNVLFGLYQPEKGEILV 63

Query: 69  AGKPYEPTAVHEVAKAGIARTFQNIRLFAEMTALENVMVGRHIRTGSGLFGAVFRTKGFK 128
            GKP + T  +   + GI    Q+  L  + T  EN+++G+              T G K
Sbjct: 64  KGKPVKITDPNVANRLGIGMVHQHFMLVEKFTVTENIILGKE------------PTAGGK 111

Query: 129 AEEAAIAKRAQELLDYVGIGKFADYKARTLSYGDQRRLEIARALATDPQLIALDEPAAGM 188
                 AK  + +    G+      K + +S G Q+R+EI + L    +++  DEP A +
Sbjct: 112 INIKKAAKAVETISKQYGLAVDPYAKIQDISVGMQQRVEILKTLYRGAEILIFDEPTAAL 171

Query: 189 NATEKVQLRELIDRIRNDNRTILLIEHDVKLVMGLCDRVTVLDYGKQI 236
              E  +L +++ ++ ++ ++I+LI H +K +M +CDR TV+  G+ I
Sbjct: 172 TPQEITELIQIMKKLVSEGKSIILITHKLKEIMEVCDRCTVIRRGRGI 219



 Score = 79.3 bits (194), Expect = 1e-19
 Identities = 55/231 (23%), Positives = 111/231 (48%), Gaps = 12/231 (5%)

Query: 22  LQALSDVGITIKRGQVYGLIGPNGAGKTTFFNVITGLYTPDAGTFELAGKPYEPTAVHEV 81
           + A++D+ + +  G++ G+ G +G G+T     ITGL  P  G  +L G+        ++
Sbjct: 270 ITAVNDLHLEVHAGEILGVAGVDGNGQTELIEAITGLRKPTGGNIQLNGQDITGLTPRKI 329

Query: 82  AKAGIARTFQNIR---LFAEMTALENVMVGRHIRTGSGLFGAVFRTKGFKAEEAAIAKRA 138
             AG+    Q+     L  + T  EN+++  + +      G +   +        I K+A
Sbjct: 330 TGAGVGHIPQDRHKHGLVLDFTVGENIVLQTYYQKPYSTSGVLNFNE--------IYKKA 381

Query: 139 QELLDYVGIGKFADYK-ARTLSYGDQRRLEIARALATDPQLIALDEPAAGMNATEKVQLR 197
            EL++   +   +++  AR LS G+Q++  IAR +   P L+   +P  G++      + 
Sbjct: 382 NELIEDYDVRTPSEHTLARALSGGNQQKAIIAREVDRSPDLLIAAQPTRGLDVGAIESIH 441

Query: 198 ELIDRIRNDNRTILLIEHDVKLVMGLCDRVTVLDYGKQIAEGNPAEVQKNE 248
             + + R+  + +LLI  ++  V+ + DR+ V+  GK +A  +  +  +NE
Sbjct: 442 HRLVKERDKGKAVLLISLELDEVLNVSDRIAVIYEGKIVAIVDADKTNENE 492


Lambda     K      H
   0.319    0.137    0.384 

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: 328
Number of extensions: 14
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 260
Length of database: 509
Length adjustment: 29
Effective length of query: 231
Effective length of database: 480
Effective search space:   110880
Effective search space used:   110880
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 (21.7 bits)
S2: 49 (23.5 bits)

This GapMind analysis is from Apr 09 2024. 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