GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Ac3H11_2562 in Mesorhizobium ciceri WSM1271

Align ABC transporter for L-Histidine, periplasmic substrate-binding component 2 (characterized)
to candidate YP_004141853.1 Mesci_2668 hypothetical protein

Query= reanno::acidovorax_3H11:Ac3H11_2562
         (321 letters)



>NCBI__GCF_000185905.1:YP_004141853.1
          Length = 335

 Score =  120 bits (302), Expect = 4e-32
 Identities = 98/316 (31%), Positives = 145/316 (45%), Gaps = 7/316 (2%)

Query: 11  LAAAAACVMALAA-PAQAQDTKIVLGMSGWTGFAPLTLADKAGIFKKNGL-DVEI-KMIP 67
           LAAA A   A AA P   +     +G+  W G+    +A+  G+FK NGL DV+I     
Sbjct: 19  LAAAPAAYAADAAIPTTPEAGAFKIGIEPWLGYGQWHVAEAKGLFKTNGLSDVQIVNFAE 78

Query: 68  QKDRHLALASKSIQCAATTVETHVAWNANGVPIVQIFQMDKSYGADGIAVRGDIKSFADL 127
            KD + ALAS  +  A     T +   A G+P+  +  +D S  AD I    D+ S ADL
Sbjct: 79  DKDINAALASGQLDAANIATHTAMGMVAAGLPVKIVLLLDVSMTADAIIAGKDVTSIADL 138

Query: 128 KGKTIGVDAPGTAPYFGLAWMLSKNGMSLKDVKTTTLSPQAAAQAFVAGQNDAAMTYEPY 187
           KGK +  +  GT     L + L++NGMS+ DVK   +    A  A +AGQ   A+TYEPY
Sbjct: 139 KGKQVAFEE-GTTSDILLKYALTRNGMSIDDVKPVPMPASDAGSALIAGQVPVAVTYEPY 197

Query: 188 LSTVRDNPAAGKILATTLDYP-MVMDTVGCDPTWLKANGKAAQALANSYFQALDMIKADP 246
           L+         K+L T  + P ++ D +      +K+      A+  S+  AL    AD 
Sbjct: 198 LTVAMAQNKDLKLLFTAGEDPGLISDVLVVRDEVIKSRPGQVLAMIKSWDAALKDYNADT 257

Query: 247 AKSNEIMGAAVKQTGEQFAKSSSFLRWQDKAANQKFFAGELTT-FMKDATAILLEAGIIR 305
                I+  AV    +    +   +R+   A N+    G+ TT    D  A    A ++ 
Sbjct: 258 PGGRAIIAKAVGSDVKDLNTAFDGVRYYSLAENKAALTGDFTTKTFADVEAAAKNAKLL- 316

Query: 306 KANEDLAVTFDASFIK 321
           +A+       D SF+K
Sbjct: 317 QADVTPEQMIDPSFVK 332


Lambda     K      H
   0.317    0.129    0.374 

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: 272
Number of extensions: 19
Number of successful extensions: 3
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: 321
Length of database: 335
Length adjustment: 28
Effective length of query: 293
Effective length of database: 307
Effective search space:    89951
Effective search space used:    89951
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 (21.7 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