GapMind for catabolism of small carbon sources

 

Aligments for a candidate for LAT2 in Pedobacter sp. GW460-11-11-14-LB5

Align Large neutral amino acids transporter small subunit 2; L-type amino acid transporter 2; Solute carrier family 7 member 8 (characterized)
to candidate CA265_RS14990 CA265_RS14990 amino acid transporter

Query= SwissProt::Q9WVR6
         (533 letters)



>lcl|FitnessBrowser__Pedo557:CA265_RS14990 CA265_RS14990 amino acid
           transporter
          Length = 480

 Score =  206 bits (525), Expect = 1e-57
 Identities = 140/464 (30%), Positives = 233/464 (50%), Gaps = 39/464 (8%)

Query: 38  KKEIGLVSACGIIVGNIIGSGIFVSPKGVLENAGSVGLALIVWIVTGVITAVGALCYAEL 97
           K+++ L  A  +++G++IGSGIF+    ++ N GS    ++VW++TGV+T   A+ Y EL
Sbjct: 11  KRKLSLFDATMLVMGSMIGSGIFIVSADIMRNLGSGYWLIVVWVITGVMTVAAAISYGEL 70

Query: 98  GVTIPKSGGDYSYVKDIFGGLAGFLRLWIAVLVIYPTNQAVIALTFSNYV---------L 148
               PK+GG Y+Y+K+IFG + GFL  W    VI     A +A+ F  +           
Sbjct: 71  SSMFPKAGGQYTYLKEIFGKMMGFLYGWGLFTVIQTGTIAAVAVAFGKFTAYLIPALNDA 130

Query: 149 QPLFPTCFPPESGLRLLAAICLLLLTWVNCSSVRWATRVQDIFTAGKLLALALIIIMGVV 208
            P+F +     + +++LA   +LLLT++N   V     +Q+IFT  K++AL  +II+G  
Sbjct: 131 APIFQSGGYKITWIQILAIGVILLLTYINTKGVESGKILQNIFTGSKIVALIGLIILGFF 190

Query: 209 QICKGEFFWLE----PKNAFENFQEPD-----------------IGLVALAFLQGSFAYG 247
            +     FW E      +AF N +                    +G +A A +   F+  
Sbjct: 191 LVKNS--FWAENLGFGSSAFNNLKTDASGNFLKSGWESISGMTIMGGIAAAMVGSVFSSV 248

Query: 248 GWNFLNYVTEELVDPYKNLPRAIFISIPLVTFVYVFANIAYVTAMSPQEL--LASNAVAV 305
            W  + +V+ E+ +P KN+ R++ +    V  +Y+  N  Y+  ++   +    ++ VAV
Sbjct: 249 AWENVTFVSGEIENPKKNVVRSMVLGTSAVMILYLLVNFIYLNTLNRDSIAFALNDRVAV 308

Query: 306 TFGEKLL--GVMAWIMPISVALSTFGGVNGSLFTSSRLFFAGAREGHLPSVLAMIHVKRC 363
              E++   G+   ++ + V +STFG VNG +   +R+F   A++G      A+ + K  
Sbjct: 309 AASEQIFGSGIGTIVIALLVMISTFGCVNGIVLAGARVFQTMAKDGMFFKA-ALKNNKNG 367

Query: 364 TPIPALLFTCLSTLLMLVTSDMYTLINYVGFINYLFYGVTVAGQIVLRWKKPDIPRPIKI 423
            P  +L    +    + ++     L++ + F+  LFY +TV G I LR K+P + RP K 
Sbjct: 368 VPEKSLWMQGIWASALCLSGQYGNLLDMISFVIVLFYMITVFGVIYLRIKQPKLERPYKT 427

Query: 424 SL--LFPIIYLLFWAFLLIFSLWSEPVVCGIGLAIMLTGVPVYF 465
            L  + PIIYLL  A   I  L  +      GL I+L GVPVYF
Sbjct: 428 WLYPITPIIYLLIGAAFCILLLIYKQQYTWPGLVIVLLGVPVYF 471


Lambda     K      H
   0.325    0.142    0.440 

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: 641
Number of extensions: 48
Number of successful extensions: 6
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: 533
Length of database: 480
Length adjustment: 34
Effective length of query: 499
Effective length of database: 446
Effective search space:   222554
Effective search space used:   222554
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 (21.6 bits)
S2: 52 (24.6 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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