GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PGA1_c07320 in Alkalihalobacterium alkalinitrilicum DSM 22532

Align Inositol transport system ATP-binding protein (characterized)
to candidate WP_078427103.1 BK574_RS00955 ABC transporter ATP-binding protein

Query= reanno::Phaeo:GFF717
         (261 letters)



>NCBI__GCF_002019605.1:WP_078427103.1
          Length = 509

 Score =  148 bits (373), Expect = 3e-40
 Identities = 82/242 (33%), Positives = 136/242 (56%), Gaps = 9/242 (3%)

Query: 7   LIRMQGIEKHFGSVIALAGVSVDVFPGECHCLLGDNGAGKSTFIKTMSGVHKPTKGDILF 66
           +I M+ I K F  ++A   V++ V  GE H LLG+NGAGKST +  + G+++P KG+IL 
Sbjct: 4   VIEMKDIRKEFPGIVANDNVTLQVKQGEIHALLGENGAGKSTLMNVLFGLYQPEKGEILV 63

Query: 67  EGQPLHFADPRDAIAAGIATVHQHLAMIPLMSVSRNFFMGNEPIR--KIGPLKLFDHDYA 124
           +G+P+   DP  A   GI  VHQH  ++   +V+ N  +G EP    KI   K      A
Sbjct: 64  KGKPVKITDPNVANRLGIGMVHQHFMLVEKFTVTENIILGKEPTAGGKINIKK------A 117

Query: 125 NRITMEEMRKMGINLRGPDQAVGTLSGGERQTVAIARAVHFGAKVLILDEPTSALGVRQT 184
            +      ++ G+ +  P   +  +S G +Q V I + ++ GA++LI DEPT+AL  ++ 
Sbjct: 118 AKAVETISKQYGLAV-DPYAKIQDISVGMQQRVEILKTLYRGAEILIFDEPTAALTPQEI 176

Query: 185 ANVLATIDKVRKQGVAVVFITHNVRHALAVGDRFTVLNRGKTLGTAQRGDISAEELQDMM 244
             ++  + K+  +G +++ ITH ++  + V DR TV+ RG+ +GT    + + + L  MM
Sbjct: 177 TELIQIMKKLVSEGKSIILITHKLKEIMEVCDRCTVIRRGRGIGTVDISESTPDSLAAMM 236

Query: 245 AG 246
            G
Sbjct: 237 VG 238



 Score = 79.7 bits (195), Expect = 1e-19
 Identities = 60/239 (25%), Positives = 104/239 (43%), Gaps = 5/239 (2%)

Query: 13  IEKHFGSVIALAGVSVDVFPGECHCLLGDNGAGKSTFIKTMSGVHKPTKGDILFEGQPLH 72
           + K    + A+  + ++V  GE   + G +G G++  I+ ++G+ KPT G+I   GQ + 
Sbjct: 263 VVKDSRDITAVNDLHLEVHAGEILGVAGVDGNGQTELIEAITGLRKPTGGNIQLNGQDIT 322

Query: 73  FADPRDAIAAGIATV----HQHLAMIPLMSVSRNFFMGNEPIRKIGPLKLFDHDYANRIT 128
              PR    AG+  +    H+H  ++   +V  N  +     +      + + +   +  
Sbjct: 323 GLTPRKITGAGVGHIPQDRHKH-GLVLDFTVGENIVLQTYYQKPYSTSGVLNFNEIYKKA 381

Query: 129 MEEMRKMGINLRGPDQAVGTLSGGERQTVAIARAVHFGAKVLILDEPTSALGVRQTANVL 188
            E +    +           LSGG +Q   IAR V     +LI  +PT  L V    ++ 
Sbjct: 382 NELIEDYDVRTPSEHTLARALSGGNQQKAIIAREVDRSPDLLIAAQPTRGLDVGAIESIH 441

Query: 189 ATIDKVRKQGVAVVFITHNVRHALAVGDRFTVLNRGKTLGTAQRGDISAEELQDMMAGG 247
             + K R +G AV+ I+  +   L V DR  V+  GK +        +  EL  +MAGG
Sbjct: 442 HRLVKERDKGKAVLLISLELDEVLNVSDRIAVIYEGKIVAIVDADKTNENELGLLMAGG 500


Lambda     K      H
   0.321    0.137    0.395 

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: 348
Number of extensions: 21
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: 261
Length of database: 509
Length adjustment: 29
Effective length of query: 232
Effective length of database: 480
Effective search space:   111360
Effective search space used:   111360
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 (21.9 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