GapMind for catabolism of small carbon sources

 

Alignments for a candidate for tnaB in Klebsiella michiganensis M5al

Align High affinity (3 (characterized)
to candidate BWI76_RS25050 BWI76_RS25050 tryptophan permease

Query= TCDB::P0AAD2
         (414 letters)



>FitnessBrowser__Koxy:BWI76_RS25050
          Length = 414

 Score =  769 bits (1986), Expect = 0.0
 Identities = 377/414 (91%), Positives = 398/414 (96%)

Query: 1   MATLTTTQTSPSLLGGVVIIGGTIIGAGMFSLPVVMSGAWFFWSMAALIFTWFCMLHSGL 60
           MATLTTT T PSL GGVVIIGGTIIGAGMFSLPVVMSGAWFFWS+AAL+FTWFCMLHSGL
Sbjct: 1   MATLTTTATRPSLFGGVVIIGGTIIGAGMFSLPVVMSGAWFFWSLAALVFTWFCMLHSGL 60

Query: 61  MILEANLNYRIGSSFDTITKDLLGKGWNVVNGISIAFVLYILTYAYISASGSILHHTFAE 120
           MILEANLNYRIGSSFDTITKDLLGKGWN++NG+SIAFVLYILTYAYISASGSILHHTF+E
Sbjct: 61  MILEANLNYRIGSSFDTITKDLLGKGWNLLNGVSIAFVLYILTYAYISASGSILHHTFSE 120

Query: 121 MSLNVPARAAGFGFALLVAFVVWLSTKAVSRMTAIVLGAKVITFFLTFGSLLGHVQPATL 180
           MSLNVPARAAGFGFALLVAF+VWLSTKAVSRMTAIVLGAKVITFFLTFGSLLGHVQP TL
Sbjct: 121 MSLNVPARAAGFGFALLVAFIVWLSTKAVSRMTAIVLGAKVITFFLTFGSLLGHVQPTTL 180

Query: 181 FNVAESNASYAPYLLMTLPFCLASFGYHGNVPSLMKYYGKDPKTIVKCLVYGTLMALALY 240
           FNVAE NASY PYLLMTLPFCLASFGYHGNVPSLMKYYGKDP+TIVKCLVYGTL+AL LY
Sbjct: 181 FNVAEKNASYLPYLLMTLPFCLASFGYHGNVPSLMKYYGKDPRTIVKCLVYGTLLALGLY 240

Query: 241 TIWLLATMGNIPRPEFIGIAEKGGNIDVLVQALSGVLNSRSLDLLLVVFSNFAVASSFLG 300
            +WLL TMGNIPRPEFIGIA+KGGNIDVLVQALSGVLNSRSLDLLLV+FSNFAVASSFLG
Sbjct: 241 VVWLLVTMGNIPRPEFIGIAQKGGNIDVLVQALSGVLNSRSLDLLLVIFSNFAVASSFLG 300

Query: 301 VTLGLFDYLADLFGFDDSAVGRLKTALLTFAPPVVGGLLFPNGFLYAIGYAGLAATIWAA 360
           VTLGLFDYLADLFGFDDSA+GR KTA+ TF PP+VGGLL+PNGFLYAIGYAGLAATIWAA
Sbjct: 301 VTLGLFDYLADLFGFDDSALGRFKTAIFTFVPPMVGGLLWPNGFLYAIGYAGLAATIWAA 360

Query: 361 IVPALLARASRKRFGSPKFRVWGGKPMIALILVFGVGNALVHILSSFNLLPVYQ 414
           IVPALLARASRKRFGSP FRVWGGKPMIAL+L+FG+GN +VH LSSFN+LP YQ
Sbjct: 361 IVPALLARASRKRFGSPLFRVWGGKPMIALVLLFGLGNVIVHFLSSFNVLPTYQ 414


Lambda     K      H
   0.328    0.142    0.434 

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: 737
Number of extensions: 24
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: 414
Length of database: 414
Length adjustment: 31
Effective length of query: 383
Effective length of database: 383
Effective search space:   146689
Effective search space used:   146689
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 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