GapMind for catabolism of small carbon sources

 

Alignments for a candidate for actP in Dietzia timorensis ID05-A0528

Align Monocarboxylic acid transporter (characterized)
to candidate WP_082908435.1 BJL86_RS04300 cation acetate symporter

Query= SwissProt::Q8NS49
         (551 letters)



>NCBI__GCF_001659785.1:WP_082908435.1
          Length = 540

 Score =  720 bits (1858), Expect = 0.0
 Identities = 369/538 (68%), Positives = 440/538 (81%), Gaps = 12/538 (2%)

Query: 14  EGVGNPILNISVFVVFIIVTMTVVLRVGKSTSESTDFYTGGASFSGTQNGLAIAGDYLSA 73
           E VG+ +LN+ VF +FI++TM +V+R   ST  + DFYT    FSGTQNG AIAGDYLSA
Sbjct: 15  EAVGSTVLNMVVFGIFIVITMGLVIRASNSTKSAADFYTASGGFSGTQNGFAIAGDYLSA 74

Query: 74  ASFLGIVGAISLNGYDGFLYSIGFFVAWLVALLLVAEPLRNVGRFTMADVLSFRLRQKPV 133
           ASFLGI GAI+L GYDGFLYSIGF VAWLVALLLVAE +RN GRFTMADVLSFRL+Q+PV
Sbjct: 75  ASFLGIAGAIALQGYDGFLYSIGFLVAWLVALLLVAELMRNTGRFTMADVLSFRLQQRPV 134

Query: 134 RVAAACGTLAVTLFYLIAQMAGAGSLVSVLLDIHEFKWQAVVVGIVGIVMIAYVLLGGMK 193
           R+AAA  TLAV LFYLIAQMAGAG LV++LL+I     Q+VVV IVG++MI YVL+GGMK
Sbjct: 135 RMAAALATLAVCLFYLIAQMAGAGGLVALLLNIDSETGQSVVVAIVGVLMILYVLIGGMK 194

Query: 194 GTTYVQMIKAVLLVGGVAIMTVLTFVKVSGGLTTLLNDAVEKHAASDYAATKGYDPTQIL 253
           GTTYVQMIKAVLLVGGV +M +L  V V G  + LL+ A+ +                + 
Sbjct: 195 GTTYVQMIKAVLLVGGVLVMCLLVLVAVRGNFSELLSAAINRSGEP------------LT 242

Query: 254 EPGLQYGATLTTQLDFISLALALCLGTAGLPHVLMRFYTVPTAKEARKSVTWAIVLIGAF 313
           +PGL+YGAT TT+LDF+SL +AL  GTAGLPHVLMRFYTVPTAKEAR+SVTWAI LIGAF
Sbjct: 243 DPGLKYGATETTKLDFLSLGIALVFGTAGLPHVLMRFYTVPTAKEARRSVTWAIALIGAF 302

Query: 314 YLMTLVLGYGAAALVGPDRVIAAPGAANAAAPLLAFELGGSIFMALISAVAFATVLAVVA 373
           YL TLVLG+GAAA+VG D + AAPG  N+AAPLLA+ LGG IFM +ISAVAFAT+LAVVA
Sbjct: 303 YLFTLVLGFGAAAMVGSDVIEAAPGGVNSAAPLLAYALGGEIFMGIISAVAFATILAVVA 362

Query: 374 GLAITASAAVGHDIYNAVIRNGQSTEAEQVRVSRITVVVIGLISIVLGILAMTQNVAFLV 433
           GLAI+ASA++ HDIYN VI++G++TE +Q++VSRITVVVIG++SIVLGI AM QN+AFLV
Sbjct: 363 GLAISASASLAHDIYNGVIKHGKATEQQQLKVSRITVVVIGIVSIVLGIGAMGQNIAFLV 422

Query: 434 ALAFAVAASANLPTILYSLYWKKFNTTGAVAAIYTGLISALLLIFLSPAVSGNDSAMVPG 493
           ALAFAVAASANLPTI+YSL+W++FNT GA+ +IY GLIS L+LIF SPA+SG+++AM+P 
Sbjct: 423 ALAFAVAASANLPTIIYSLFWRRFNTRGALFSIYGGLISTLVLIFFSPAISGSETAMLPN 482

Query: 494 ADWAIFPLKNPGLVSIPLAFIAGWIGTLVGKPDNMDDLAAEMEVRSLTGVGVEKAVDH 551
           ADWAIFPL NPG++SIP  F+ G IGT +GK D   D  AEMEVRS+TGVGVEKAV H
Sbjct: 483 ADWAIFPLSNPGIISIPFGFLMGIIGTFLGKSDEFPDKEAEMEVRSMTGVGVEKAVQH 540


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: 758
Number of extensions: 27
Number of successful extensions: 2
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: 540
Length adjustment: 35
Effective length of query: 516
Effective length of database: 505
Effective search space:   260580
Effective search space used:   260580
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: 52 (24.6 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