GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hisN in Thiomicrorhabdus arctica DSM 13458

Align Histidinol-phosphatase; Hol-Pase; Histidinol-phosphate phosphatase; EC 3.1.3.15 (characterized)
to candidate WP_019556519.1 F612_RS0104285 HAD-IB family hydrolase

Query= SwissProt::Q9I6F6
         (217 letters)



>NCBI__GCF_000381085.1:WP_019556519.1
          Length = 217

 Score =  227 bits (579), Expect = 1e-64
 Identities = 113/217 (52%), Positives = 142/217 (65%)

Query: 1   MRLALFDLDNTLLAGDSDHSWGEWLCQRGLVDAAEYQARNDAFYADYVAGKLDVLAYQAF 60
           M L +FDLDNTL+ GDSD+ WG +L +   VDA E+ A+N+ FY DY AG LD++AYQ F
Sbjct: 1   MALVIFDLDNTLIGGDSDYLWGAFLVENQYVDATEFAAQNEQFYEDYKAGTLDIMAYQRF 60

Query: 61  TQAILGRTEMAQLETWHRQFMQEVIEPIVLAKGEALLAEHRAAGDRLVIITATNRFVTGP 120
               L +  M  L  WH QFMQ  IEPIVL K  AL+ +H+  GDR++IITATN F+T  
Sbjct: 61  ALKPLSQHSMETLNEWHAQFMQTFIEPIVLPKALALVNDHKNKGDRVIIITATNTFITRR 120

Query: 121 IAERLGVETLIATECEMRDGRYTGQTFDVPCFQGGKVVRLQRWLDENGLDLEGASFYSDS 180
           I  R G+  L+ T  E+ + RYTG+   +P FQ GKV RL  WL+   + L G+ FYSDS
Sbjct: 121 IGLRYGITELLGTNGEIVNKRYTGEVEGIPTFQAGKVTRLNEWLERENVSLAGSVFYSDS 180

Query: 181 LNDLPLLEKVSRPVAVDPDPRLRAEAEKRGWPIISLR 217
            NDLPLL+ V  PV VD D +L   A+ RGWP ISLR
Sbjct: 181 FNDLPLLDIVDNPVVVDGDDKLLNIAKTRGWPSISLR 217


Lambda     K      H
   0.321    0.138    0.418 

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: 176
Number of extensions: 2
Number of successful extensions: 1
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: 217
Length of database: 217
Length adjustment: 22
Effective length of query: 195
Effective length of database: 195
Effective search space:    38025
Effective search space used:    38025
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 (21.9 bits)
S2: 45 (21.9 bits)

This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.

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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