GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mt2d in Marinicella litoralis KMM 3900

Align mannitol 2-dehydrogenase (NADP+) (EC 1.1.1.138) (characterized)
to candidate WP_099019607.1 CCS90_RS11000 L-threonine 3-dehydrogenase

Query= BRENDA::Q1ACW3
         (345 letters)



>NCBI__GCF_002591915.1:WP_099019607.1
          Length = 340

 Score =  150 bits (379), Expect = 5e-41
 Identities = 98/278 (35%), Positives = 145/278 (52%), Gaps = 14/278 (5%)

Query: 7   MKALRYDKPESYAVVE-VPLPTLRDNDVLIKVKACGVCGTDLHIHE-GEFIAKF---PLI 61
           MKAL   KPE    +E VP+P +  NDVLIK++   +CGTDLHI++  E+ AK    PL+
Sbjct: 1   MKALVKKKPELGIWMEDVPMPEMGHNDVLIKIEKTAICGTDLHIYKWDEWSAKAIKPPLV 60

Query: 62  PGHETVGVVAAIGKDVKGFTVGERVCADNSELCNECFYCRRGQLLLCEKFEAHGVTMDGG 121
            GHE VG +  +G +VKG+ VG+RV A+   +C  C  CR G   LC   +  GV  +G 
Sbjct: 61  IGHEFVGHIVDMGSEVKGYEVGQRVSAEGHIVCGVCRNCRAGTPHLCPNTQGIGVNRNGA 120

Query: 122 FAEYCAYPAGKVFKI-HNLSDVDATLLEPASCAAH-GLEKIAPKIGSSVLMFGAGPTGLC 179
           FAE+ + P   ++ +   +    A   +P   AAH  LE     +G  VL+ GAGP G+ 
Sbjct: 121 FAEFISMPVQNLWPVPDKIPSNLAAFFDPFGNAAHCALE--YDMVGEDVLITGAGPIGII 178

Query: 180 LAQL-PHNGASHVVIAAPEGLKMDLAKKLDCADIYVPLSRSNPQAQFDQIKSDNPYGFDI 238
              +  H GA +VVI      ++ LAK +             P      +K  N  GFD+
Sbjct: 179 ATGICKHVGARNVVITDVNDYRLSLAKDMGATRCVNVTKEKLPAV----MKEMNITGFDL 234

Query: 239 VVEATGSPKILEDAINYVRRGGKLVVYGVYSDAARVSW 276
            +E +G+P    D +N +  GGK+ + G+  D  +++W
Sbjct: 235 GMEMSGNPMAFNDMLNSMYNGGKITLLGMLPDHTQINW 272


Lambda     K      H
   0.320    0.138    0.420 

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: 331
Number of extensions: 21
Number of successful extensions: 4
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: 345
Length of database: 340
Length adjustment: 29
Effective length of query: 316
Effective length of database: 311
Effective search space:    98276
Effective search space used:    98276
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 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