GapMind for catabolism of small carbon sources

 

Aligments for a candidate for hutX in Sinorhizobium meliloti 1021

Align HutX aka HISX, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized)
to candidate SM_b21572 SM_b21572 amino acid uptake ABC transporter substrate-binding protein precursor

Query= TCDB::Q9KKE3
         (346 letters)



>lcl|FitnessBrowser__Smeli:SM_b21572 SM_b21572 amino acid uptake ABC
           transporter substrate-binding protein precursor
          Length = 333

 Score =  171 bits (432), Expect = 3e-47
 Identities = 116/349 (33%), Positives = 180/349 (51%), Gaps = 27/349 (7%)

Query: 8   MRLTFAAAGLMLA--ASASGANASYCGDGKTVTFAGIDWESGAFITEVMKTILSKGYDCQ 65
           M+   A+  LML   A AS ++A+ CG   TVT A ++W+S   ++ + K IL++GY C 
Sbjct: 1   MKKLLASTCLMLGLIAGASTSSAAECG---TVTIASMNWQSAEVLSNLDKFILNEGYGCS 57

Query: 66  VDSIPGNSV-TLEQATANNDVQIFAEEWLGR-SDVWNKAVEEKKVIAVGKTFV-GASEGW 122
            +   G++V T+          I  E W+    DV  K  ++ ++I VG     G  +GW
Sbjct: 58  AEITIGDTVPTITSMAEKGQPDIAPEAWIDLLPDVVKKGQDDGRIITVGSPLPDGGVQGW 117

Query: 123 FVPDYVVHGDPARNIEAKAPDLKSVSQLTDPKIAEIFADPEEPSKGRFLNCPSGWTCEGV 182
           ++P Y+    P         D+K++      K  E+F   E+PSKG  LN P GW    V
Sbjct: 118 WIPQYLADAHP---------DIKTIGDAL--KHPELFPASEDPSKGAILNGPQGWGGTVV 166

Query: 183 STAKLEAY---KLGETYVNFRPGTGTALDAAITSAYLQGEPIFFYYWSPTAILGKFKLIQ 239
           +T    A+   K G T V+   G+   LD AI  AY + E +  YYWSPTA+LGK+K+++
Sbjct: 167 TTQLFSAFDGEKAGFTLVD--TGSAAGLDGAIAKAYERKEGLLTYYWSPTALLGKYKMVK 224

Query: 240 LEEPAYNEAC-WKELSSANGKRD-EGCAFPSVDVAYGVNSTFASEA-PEIVEILEKATFP 296
           L+    ++A  WK  ++     D +  A+P   +   V   F+    PE+++ L K ++ 
Sbjct: 225 LDPGVPHDAAEWKRCNTVADCPDPKPNAWPVDTIVTLVAKPFSERVGPEVMDYLTKRSWS 284

Query: 297 LDEVNASLAYMADNKVDATAAAAEFLKTKGDIWSKWVSDEARGKIEAGL 345
            + V+  +A+M DN+      A  FL+   D+WSKWVS EA  KI+A L
Sbjct: 285 NETVSQLMAWMTDNQASGEEGAKRFLEENEDMWSKWVSPEAAEKIKAAL 333


Lambda     K      H
   0.314    0.130    0.391 

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: 344
Number of extensions: 20
Number of successful extensions: 5
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: 346
Length of database: 333
Length adjustment: 28
Effective length of query: 318
Effective length of database: 305
Effective search space:    96990
Effective search space used:    96990
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: 42 (22.0 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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