GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PS417_11890 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::WCS417:GFF2332
         (517 letters)



>NCBI__GCF_002019605.1:WP_078427103.1
          Length = 509

 Score =  317 bits (813), Expect = 5e-91
 Identities = 180/503 (35%), Positives = 292/503 (58%), Gaps = 12/503 (2%)

Query: 22  YLLEIVNISKGFPGVVALADVQLRVRPGTVLALMGENGAGKSTLMKIIAGIYQPDAGEIR 81
           Y++E+ +I K FPG+VA  +V L+V+ G + AL+GENGAGKSTLM ++ G+YQP+ GEI 
Sbjct: 3   YVIEMKDIRKEFPGIVANDNVTLQVKQGEIHALLGENGAGKSTLMNVLFGLYQPEKGEIL 62

Query: 82  LRGKPIVFETPLAAQKAGIAMIHQELNLMPHMSIAENIWIGREQLNSLHMVNHREMHRCT 141
           ++GKP+    P  A + GI M+HQ   L+   ++ ENI +G+E   +   +N ++  +  
Sbjct: 63  VKGKPVKITDPNVANRLGIGMVHQHFMLVEKFTVTENIILGKEP-TAGGKINIKKAAKAV 121

Query: 142 AELLARLRINLDPEEQVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITEKEVAHLFS 201
             +  +  + +DP  ++ ++S+  +Q VEI K +   ++ILI DEPT+A+T +E+  L  
Sbjct: 122 ETISKQYGLAVDPYAKIQDISVGMQQRVEILKTLYRGAEILIFDEPTAALTPQEITELIQ 181

Query: 202 IIADLKSQGKGIVYITHKMNEVFAIADEVAVFRDGHYIGLQRADSMNSDSLISMMVGREL 261
           I+  L S+GK I+ ITHK+ E+  + D   V R G  IG         DSL +MMVGRE+
Sbjct: 182 IMKKLVSEGKSIILITHKLKEIMEVCDRCTVIRRGRGIGTVDISESTPDSLAAMMVGREV 241

Query: 262 SQLFPLRETPI--GDLLLTVRDLTLDG-----VFKDVSFDLHAGEILGIAGLMGSGRTNV 314
           +  F + + P    D +L ++DL +          D+  ++HAGEILG+AG+ G+G+T +
Sbjct: 242 N--FSVEKDPAQPKDAVLQIKDLVVKDSRDITAVNDLHLEVHAGEILGVAGVDGNGQTEL 299

Query: 315 AETIFGITPSSSGQITLDGKAVRISDPHMAIEKGFALLTEDRKLSGLFPCLSVLENMEMA 374
            E I G+   + G I L+G+ +    P      G   + +DR   GL    +V EN+ + 
Sbjct: 300 IEAITGLRKPTGGNIQLNGQDITGLTPRKITGAGVGHIPQDRHKHGLVLDFTVGENIVLQ 359

Query: 375 VL--PHYTGNGFIQQKALRALCEDMCKKLRVKTPSLEQCIDTLSGGNQQKALLARWLMTN 432
                 Y+ +G +    +     ++ +   V+TPS       LSGGNQQKA++AR +  +
Sbjct: 360 TYYQKPYSTSGVLNFNEIYKKANELIEDYDVRTPSEHTLARALSGGNQQKAIIAREVDRS 419

Query: 433 PRLLILDEPTRGIDVGAKAEIYRLIAFLASEGMAVIMISSELPEVLGMSDRVMVMHEGEL 492
           P LLI  +PTRG+DVGA   I+  +     +G AV++IS EL EVL +SDR+ V++EG++
Sbjct: 420 PDLLIAAQPTRGLDVGAIESIHHRLVKERDKGKAVLLISLELDEVLNVSDRIAVIYEGKI 479

Query: 493 MGTLDRSEATQEKVMQLASGMTA 515
           +  +D  +  + ++  L +G +A
Sbjct: 480 VAIVDADKTNENELGLLMAGGSA 502


Lambda     K      H
   0.320    0.136    0.381 

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: 595
Number of extensions: 24
Number of successful extensions: 8
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: 517
Length of database: 509
Length adjustment: 35
Effective length of query: 482
Effective length of database: 474
Effective search space:   228468
Effective search space used:   228468
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: 52 (24.6 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