GapMind for catabolism of small carbon sources

 

Alignments for a candidate for HSERO_RS00900 in Caldicellulosiruptor hydrothermalis 108

Align ABC-type branched-chain amino acid transport system, ATPase component protein (characterized, see rationale)
to candidate WP_013402887.1 CALHY_RS04860 ABC transporter ATP-binding protein

Query= uniprot:D8IUY7
         (241 letters)



>NCBI__GCF_000166355.1:WP_013402887.1
          Length = 503

 Score = 98.2 bits (243), Expect = 3e-25
 Identities = 64/214 (29%), Positives = 109/214 (50%), Gaps = 4/214 (1%)

Query: 5   ILKVQQLSVAYGGIQAVKGIDLEVNEGELVTLIGANGAGKTTTLKAITGTLPASRVEGHI 64
           IL+V+ +S  +G IQA   + L+V +GE+  ++G NGAGK+T +  I G        G I
Sbjct: 4   ILQVKDISKRFGNIQANDNVCLDVKKGEVHAILGENGAGKSTLMNIIYGLYTPD--SGEI 61

Query: 65  EYLGQPLKGKKSFELVKDKLAMVPEGRGVFTRMSIQENLLMGAYTSDDKGQIAADIDKWF 124
            + GQ L+ K   E ++  + MV +   +    ++ EN+++G      +  +     K  
Sbjct: 62  YFEGQKLEVKGPHEAIEKGIGMVHQHFMLIPVFTVAENIVLGFEPKGFRFNVQEAEKKIL 121

Query: 125 AVFPR--LKERAAQMAGTLSGGEQQMLAMARALMSHPKLLLLDEPSMGLSPIMVEKIFEV 182
            +  +  L+       G LS G QQ + + +A     +LL+LDEP+  L+P    ++F++
Sbjct: 122 EISKKYNLEIDPKAKVGDLSVGMQQRVEILKAFYRDARLLILDEPTAMLTPQETRELFKI 181

Query: 183 IRNVSAQGITILLVEQNAKLALEAAHRGYVMESG 216
           I N+ AQGI+IL +       +E + R  VM  G
Sbjct: 182 INNLKAQGISILFISHKLDEVMEISDRVTVMRRG 215



 Score = 79.3 bits (194), Expect = 1e-19
 Identities = 62/226 (27%), Positives = 103/226 (45%), Gaps = 15/226 (6%)

Query: 5   ILKVQQLSVAY-GGIQAVKGIDLEVNEGELVTLIGANGAGKTTTLKAITGTLPASRVEGH 63
           +LKV+ LSV    G++ VK +  EV  GE+  + G +G G+   ++AI G + ++   G 
Sbjct: 255 VLKVENLSVKLKNGVEKVKDVSFEVRRGEIFGIAGVDGNGQNELVEAIVGLISST---GK 311

Query: 64  IEYLGQPLKGKKSFELVKDKLAMVPEGR---GVFTRMSIQENLLMGAYTSDDKGQ----- 115
           I + GQ ++   + +  +  +A +P  R   G+    ++ EN+++  Y  +         
Sbjct: 312 IIFNGQEIQNLPTRKRYEKGIAYIPADRQQDGLVLNFTVAENIVLKRYYKNPYSNRGFLN 371

Query: 116 ---IAADIDKWFAVFPRLKERAAQMAGTLSGGEQQMLAMARALMSHPKLLLLDEPSMGLS 172
              I  + D+    F          A  LSGG QQ + +AR   S P LL+  +P+ G+ 
Sbjct: 372 YKVITLEADRLIHEFDVRPPDYKLFAKNLSGGNQQKVILAREFSSSPDLLIAVQPTRGMD 431

Query: 173 PIMVEKIFEVIRNVSAQGITILLVEQNAKLALEAAHRGYVMESGLI 218
              +E I   +  +   G  ILLV       L  + R  VM SG I
Sbjct: 432 VGAIEYIHRKLIELRDSGKAILLVSLELDEILNLSDRIAVMYSGRI 477


Lambda     K      H
   0.317    0.134    0.365 

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: 253
Number of extensions: 17
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: 241
Length of database: 503
Length adjustment: 29
Effective length of query: 212
Effective length of database: 474
Effective search space:   100488
Effective search space used:   100488
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 49 (23.5 bits)

This GapMind analysis is from Sep 24 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