GapMind for catabolism of small carbon sources

 

Alignments for a candidate for thuK in Magnetospirillum magneticum AMB-1

Align ABC transporter (characterized, see rationale)
to candidate WP_011385763.1 AMB_RS17210 molybdenum import ATP-binding protein ModC

Query= uniprot:A0A166QFW2
         (381 letters)



>NCBI__GCF_000009985.1:WP_011385763.1
          Length = 363

 Score =  140 bits (354), Expect = 4e-38
 Identities = 91/277 (32%), Positives = 148/277 (53%), Gaps = 26/277 (9%)

Query: 8   NVNKQLGGMRILRDVSLEIAAGEFVVFVGPSGCGKSTLLRLIAGLDSICGGDLLIDGRRV 67
           ++ ++ G  R+  DV L    G   ++ G SG GK++++ ++AGL     G + +DGR +
Sbjct: 5   DLRRRQGEFRL--DVRLSAGPGVTALY-GRSGSGKTSVINMVAGLSRPDEGSISVDGRVL 61

Query: 68  ND------LEPRERGVGMVFQSYALYPHMSVYDNISFGLKLAKTDKTSLRERVLKTAQIL 121
            D      L P  R +G VFQ + L+PH+SV  N+ FG KL  + + +  + + K  ++L
Sbjct: 62  FDSRSGIDLPPEARRLGYVFQEHRLFPHLSVRGNLEFGQKLLPSAERT--QSLDKVVELL 119

Query: 122 QLDKLLQRKPKELSGGQRQRVAMGRAMAREPDILLFDEPLSNLDASLRVQMRNEIARLHD 181
            ++ LL R+P +LSGG++QRVA+GRA+   P ILL DEPL+ LD + + ++   IA+L  
Sbjct: 120 GIESLLDRRPAKLSGGEKQRVAIGRALLASPRILLMDEPLAALDPARKAEVLPFIAQLAR 179

Query: 182 RLGSTMIYVTHDQVEAMTLADKIVVLNGGRVEQVGSPRELYERPASRFVAGFLGSPRMNF 241
           R    ++YV+H   E + LAD + +++GG+V   G    L            +G P +  
Sbjct: 180 RFSVPILYVSHSMDEVLRLADTLALMDGGKVAASGPLESL------------MGDPGLRP 227

Query: 242 LSARLQTPGETSLV---DTLVWGITSLPFDSSNLAAG 275
           L+ R +       V       +GI+ L FD   L  G
Sbjct: 228 LTGRYEAGAVIGAVVSSHDSGFGISRLAFDGGTLIVG 264


Lambda     K      H
   0.320    0.137    0.394 

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: 289
Number of extensions: 11
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: 381
Length of database: 363
Length adjustment: 30
Effective length of query: 351
Effective length of database: 333
Effective search space:   116883
Effective search space used:   116883
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: 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:

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