Aligments for a candidate for mctP in Paraburkholderia bryophila 376MFSha3.1

GapMind for catabolism of small carbon sources

Aligments for a candidate for mctP in Paraburkholderia bryophila 376MFSha3.1

Align Na+/solute symporter (characterized, see rationale)
to candidate H281DRAFT_00283 H281DRAFT_00283 solute:Na+ symporter, SSS family

Query= uniprot:B2T7V3
         (493 letters)



>FitnessBrowser__Burk376:H281DRAFT_00283
          Length = 516

 Score =  535 bits (1377), Expect = e-156
 Identities = 277/497 (55%), Positives = 353/497 (71%), Gaps = 24/497 (4%)

Query: 7   VNPVAMTVFIAFFVLVTVIGFFAARWKRGDLTQLHEWGLGGRQFGTVISWFLVGGDFYTA 66
           +N +A  VF+ FF+ VT++GF AA W+RGDL  L EWGLGGR+FGT+++WFL+GGD YTA
Sbjct: 1   MNAIATFVFVLFFIGVTILGFIAAHWRRGDLAHLEEWGLGGRRFGTIVTWFLLGGDLYTA 60

Query: 67  YTVIAVPALVYSVGAYGFFALPYTIIVYPFVFAVMPKLWKIAHAKNHITAADYVQGEYGG 126
           YT IAVPALV+  GA GFFALPYTI++YPF F V PKLW IA  + ++T+AD+V   YG 
Sbjct: 61  YTFIAVPALVFGAGATGFFALPYTILIYPFAFVVFPKLWSIAKRQGYVTSADFVSARYGS 120

Query: 127 KWFPAAVAITGIVATMPYIALQLVGMQVVIKGL-----GVTGEMPLIVAFVILALYTYAS 181
           +    A+A+TGIVATMPYIALQLVG++VVI  L     G  G++PLI+AF ILA YTY S
Sbjct: 121 RMLALAIAVTGIVATMPYIALQLVGIEVVIGALGFDTKGFVGDLPLIIAFAILAAYTYTS 180

Query: 182 GLRAPAMIAFVKDIMIYIVVIAAVWLIPAKLGGYAHVF---DAADTYFKAKGGATGIILK 238
           GLRAPAMIA VKD++IYI + AA+ +IP +LGG+ H+F     A    KA       +  
Sbjct: 181 GLRAPAMIAVVKDVLIYITIFAAIIVIPPQLGGFGHIFATVPPAKLLLKAPD-----VSS 235

Query: 239 PTQFTAYASLALGSALAAFMYPHTMTAVLSSSSANTVRKNAIFLPAYTLLLGLIALLGYM 298
              ++AYA+LA+GSALA F+YPH++TAVLSS S NT+R+N   LPAY+L+LGL+ALLG+M
Sbjct: 236 LNGYSAYATLAVGSALALFLYPHSITAVLSSKSGNTIRRNMAMLPAYSLVLGLLALLGFM 295

Query: 299 AIAAGV----------HVKSASDMVPALFNTLFPSWFVGFAAAAIAISALVPAAIMSIGA 348
           A+A+GV               +  VPALF   FPSWFVG A AAI I ALVPAAIMSI A
Sbjct: 296 ALASGVKDMPEFAPYFKAFGPNFAVPALFLHFFPSWFVGVAFAAIGIGALVPAAIMSIAA 355

Query: 349 ANLFTRNLWRPLVSPNISPEGEASTAKIVSLVVKFGALLFIVFLPTQYAIDLQLLGGVWI 408
           ANL+TRN+ +  V+ N++ E E + AK+VSL+VK GA+ FI+ LP  YAI LQLLGG+WI
Sbjct: 356 ANLYTRNIHKEFVNRNMTHEQETNVAKLVSLIVKVGAVAFILGLPLTYAIQLQLLGGIWI 415

Query: 409 LQIFPAIVFSLYTRRLNTPGLFLGWLAGIVLGTGLAISQGLK-PVFALHLGDAVYPVYIG 467
           +Q  PAIV  LYTR L+  GL LGW  GI  GT +A+S  L   +F +HL     P Y  
Sbjct: 416 IQTLPAIVLGLYTRVLDYRGLLLGWAVGIATGTWMAVSLKLAGSIFTIHLFGMAIPGYAA 475

Query: 468 LIALTVNIVVSFVVSVL 484
           + +L VN+VV+ VVS+L
Sbjct: 476 VWSLIVNLVVAVVVSLL 492


Lambda     K      H
   0.328    0.141    0.431 

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: 868
Number of extensions: 48
Number of successful extensions: 5
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: 493
Length of database: 516
Length adjustment: 34
Effective length of query: 459
Effective length of database: 482
Effective search space:   221238
Effective search space used:   221238
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 (21.8 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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Steps (tab-delimited)
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Protein sequences (fasta format)
Organisms (tab-delimited)
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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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

GapMind for catabolism of small carbon sources