GapMind for catabolism of small carbon sources

 

Alignments for a candidate for actP in Knoellia flava TL1

Align Monocarboxylic acid transporter (characterized)
to candidate WP_035949051.1 N798_RS12935 cation acetate symporter

Query= SwissProt::Q8NS49
         (551 letters)



>NCBI__GCF_000768675.1:WP_035949051.1
          Length = 551

 Score =  630 bits (1625), Expect = 0.0
 Identities = 334/561 (59%), Positives = 415/561 (73%), Gaps = 20/561 (3%)

Query: 1   MNSTILLAQDAVSEGVGNPILNISVFVVFIIVTMTVVLRVGKSTSESTDFYTGGASFSGT 60
           M S +     A +  VG+P LNI++F  F++VT+ V++++      + +FYT    FSG 
Sbjct: 1   MTSFLSAGLPAEATKVGSPALNIAIFAGFVLVTLVVIVKLASGKKSAGEFYTASGGFSGR 60

Query: 61  QNGLAIAGDYLSAASFLGIVGAISLNGYDGFLYSIGFFVAWLVALLLVAEPLRNVGRFTM 120
           QNG+AIAGDYLSAASFLGI GAI+L GYDGFLYSIGF VAWLVALLLVAE +RN GR TM
Sbjct: 61  QNGIAIAGDYLSAASFLGIAGAIALQGYDGFLYSIGFLVAWLVALLLVAELMRNTGRLTM 120

Query: 121 ADVLSFRLRQKPVRVAAACGTLAVTLFYLIAQMAGAGSLVSVLLDIHEFKWQAVVVGIVG 180
           ADVLS+RL+Q+PVR+A A   LAV+ FYL+AQMAGAG LVS+LL +     Q +V+ +VG
Sbjct: 121 ADVLSYRLKQRPVRIATATSVLAVSFFYLLAQMAGAGGLVSLLLGVEGEGAQNIVIAVVG 180

Query: 181 IVMIAYVLLGGMKGTTYVQMIKAVLLVGGVAIMTVLTFVKVSGGLTTLLNDAVEKHAASD 240
           IVMIAYVL+GGM+GTT+VQ+IKAVLL+   AIMTV    K    L+ L + A++ +    
Sbjct: 181 IVMIAYVLIGGMRGTTWVQIIKAVLLIAATAIMTVWVLGKYGFNLSGLFDAAIQNNPKVG 240

Query: 241 YAATKGYDPTQILEPGLQYGATLTTQLDFISLALALCLGTAGLPHVLMRFYTVPTAKEAR 300
                     ++LEPG++YG + TT++DFISL+LAL LGTAGLPHVL RFYTVPT+K+AR
Sbjct: 241 ---------EKLLEPGVKYGVSTTTKIDFISLSLALVLGTAGLPHVLQRFYTVPTSKQAR 291

Query: 301 KSVTWAIVLIGAFYLMTLVLGYGAAALVGPDRVIAAPGAANAAAPLLAFELGGSIFMALI 360
           KSV WAI LIG FYL+TLV+GYGA ALVG + +  APG ANAAAPLLAFELGGS F+ ++
Sbjct: 292 KSVEWAIWLIGGFYLLTLVVGYGAGALVGAEEINKAPGKANAAAPLLAFELGGSPFLGIV 351

Query: 361 SAVAFATVLAVVAGLAITASAAVGHDIYNAVIRNGQSTEAEQVRVSRITVVVIGLISIVL 420
           S +AFAT+LAVVAGL ITASA   HDIY  VI+ G +T   +VRV+RI+ V IG+I+I+ 
Sbjct: 352 SGIAFATILAVVAGLTITASATFAHDIYKEVIKRGDTTSDNEVRVARISAVAIGIIAILG 411

Query: 421 GILAMTQNVAFLVALAFAVAASANLPTILYSLYWKKFNTTGAVAAIYTGLISALLLIFLS 480
           G+ A +QN+AFLVALAFAVAASANLPTILYSL+WK+FNT GA+ +IY GLIS + LI  S
Sbjct: 412 GMFAKSQNIAFLVALAFAVAASANLPTILYSLFWKRFNTRGALWSIYGGLISTIGLIIFS 471

Query: 481 PAVSGN--------DSAMV--PGADWAIFPLKNPGLVSIPLAFIAGWIGTLVGKPDNMDD 530
           P VSG           +M+  P  D++ FPL NPGLV+IPLAF  GW+GT+     N   
Sbjct: 472 PVVSGKAPLPGTTVSPSMITNPDIDFSWFPLDNPGLVTIPLAFFLGWLGTVTSSEYNAQK 531

Query: 531 LAAEMEVRSLTGVGVEKAVDH 551
             AEMEVRSLTG GV KA+DH
Sbjct: 532 Y-AEMEVRSLTGHGVAKALDH 551


Lambda     K      H
   0.324    0.138    0.393 

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: 754
Number of extensions: 33
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: 551
Length of database: 551
Length adjustment: 36
Effective length of query: 515
Effective length of database: 515
Effective search space:   265225
Effective search space used:   265225
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.5 bits)
S2: 53 (25.0 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