GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ARO8 in Oceanisphaera arctica V1-41

Align branched-chain-amino-acid transaminase (EC 2.6.1.42) (characterized)
to candidate WP_104486877.1 UN63_RS11415 branched-chain amino acid transaminase

Query= BRENDA::P0AB80
         (309 letters)



>NCBI__GCF_002936955.1:WP_104486877.1
          Length = 307

 Score =  431 bits (1108), Expect = e-125
 Identities = 197/302 (65%), Positives = 248/302 (82%)

Query: 6   ADYIWFNGEMVRWEDAKVHVMSHALHYGTSVFEGIRCYDSHKGPVVFRHREHMQRLHDSA 65
           A YIWFNG+MV WE A+VHVMSHALHYG+SVFEGIR Y++ +GP++FR  EH+QRL DSA
Sbjct: 4   AKYIWFNGDMVPWEKAQVHVMSHALHYGSSVFEGIRAYETPRGPMIFRLEEHVQRLFDSA 63

Query: 66  KIYRFPVSQSIDELMEACRDVIRKNNLTSAYIRPLIFVGDVGMGVNPPAGYSTDVIIAAF 125
           KIYR  +  + +ELM+ACR  + +N L SAY+RPL+F+G+VGMG+N P     DVI+AA 
Sbjct: 64  KIYRMKIPYTHEELMDACRKAVSENELNSAYLRPLVFIGNVGMGLNAPKDVPCDVIVAAI 123

Query: 126 PWGAYLGAEALEQGIDAMVSSWNRAAPNTIPTAAKAGGNYLSSLLVGSEARRHGYQEGIA 185
           PWGAYLG E LE+G+D  V+SWNR APNT+PT AKAGGNYLSS L+  EA+RHGY EGI+
Sbjct: 124 PWGAYLGEEGLERGVDVCVTSWNRLAPNTMPTGAKAGGNYLSSQLISGEAKRHGYDEGIS 183

Query: 186 LDVNGYISEGAGENLFEVKDGVLFTPPFTSSALPGITRDAIIKLAKELGIEVREQVLSRE 245
           LDV+G++SEGAGENLF +K+ VL+TPP T+  LPGITRD ++ LA+E G +VRE+ +SRE
Sbjct: 184 LDVHGHLSEGAGENLFLIKNKVLYTPPVTACILPGITRDTLMTLAREAGYQVREEAISRE 243

Query: 246 SLYLADEVFMSGTAAEITPVRSVDGIQVGEGRCGPVTKRIQQAFFGLFTGETEDKWGWLD 305
           +LYLADE+FM+GTAAE+TPVRSVDGI++G G+ GP+T  +Q+AFFGLF G T DKWGWL 
Sbjct: 244 ALYLADEMFMTGTAAEVTPVRSVDGIELGAGKRGPITTELQKAFFGLFDGSTRDKWGWLT 303

Query: 306 QV 307
            V
Sbjct: 304 PV 305


Lambda     K      H
   0.319    0.136    0.413 

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: 365
Number of extensions: 9
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: 309
Length of database: 307
Length adjustment: 27
Effective length of query: 282
Effective length of database: 280
Effective search space:    78960
Effective search space used:    78960
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: 48 (23.1 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