GapMind for catabolism of small carbon sources

 

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

Align Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale)
to candidate WP_011385763.1 AMB_RS17210 molybdenum import ATP-binding protein ModC

Query= uniprot:D4GP38
         (383 letters)



>NCBI__GCF_000009985.1:WP_011385763.1
          Length = 363

 Score =  140 bits (353), Expect = 6e-38
 Identities = 75/186 (40%), Positives = 117/186 (62%), Gaps = 9/186 (4%)

Query: 34  LVGPSGCGKSTTLRMLAGLETPTSGDIYIGGDHMNYR------VPQNRDIAMVFQDYALY 87
           L G SG GK++ + M+AGL  P  G I + G  +          P+ R +  VFQ++ L+
Sbjct: 28  LYGRSGSGKTSVINMVAGLSRPDEGSISVDGRVLFDSRSGIDLPPEARRLGYVFQEHRLF 87

Query: 88  PHMTVRQNIRFGLEEEEGYTSAERDERVVEVAETLGIADLLDRKPDELSGGQQQRVALGR 147
           PH++VR N+ FG   ++   SAER + + +V E LGI  LLDR+P +LSGG++QRVA+GR
Sbjct: 88  PHLSVRGNLEFG---QKLLPSAERTQSLDKVVELLGIESLLDRRPAKLSGGEKQRVAIGR 144

Query: 148 AIVRDPEVFLMDEPLSNLDAKLRAEMRTELQNLQDQLAVTTVYVTHNQTEAMTMADRIAV 207
           A++  P + LMDEPL+ LD   +AE+   +  L  + +V  +YV+H+  E + +AD +A+
Sbjct: 145 ALLASPRILLMDEPLAALDPARKAEVLPFIAQLARRFSVPILYVSHSMDEVLRLADTLAL 204

Query: 208 MDDGEL 213
           MD G++
Sbjct: 205 MDGGKV 210


Lambda     K      H
   0.317    0.135    0.386 

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: 288
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: 383
Length of database: 363
Length adjustment: 30
Effective length of query: 353
Effective length of database: 333
Effective search space:   117549
Effective search space used:   117549
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: 50 (23.9 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