GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mctC in Burkholderia phytofirmans PsJN

Align Monocarboxylic acid transporter (characterized)
to candidate BPHYT_RS25605 BPHYT_RS25605 symporter

Query= SwissProt::Q8NS49
         (551 letters)



>FitnessBrowser__BFirm:BPHYT_RS25605
          Length = 516

 Score =  394 bits (1011), Expect = e-114
 Identities = 214/532 (40%), Positives = 321/532 (60%), Gaps = 37/532 (6%)

Query: 20  ILNISVFVVFIIVTMTVVLRVGKSTSESTDFYTGGASFSGTQNGLAIAGDYLSAASFLGI 79
           +L I +F++ + VT+ +     + T  +++FY  G + S  +NG A+AGD++SAA+FLG 
Sbjct: 3   LLTIVIFMIILAVTLMITYWAARRTRTTSEFYAAGGNLSARENGFALAGDWMSAAAFLGF 62

Query: 80  VGAISLNGYDGFLYSIGFFVAWLVALLLVAEPLRNVGRFTMADVLSFRLRQKPVRVAAAC 139
            G +SL G DG LY++    A+LV L+L+AEP+RN GR+T  DV++ R+++   R+A   
Sbjct: 63  SGLVSLYGMDGSLYAVAALAAFLVVLMLIAEPVRNTGRYTFGDVIAERMKRPGARLATIV 122

Query: 140 GTLAVTLFYLIAQMAGAGSLVSVLLDIHEFKWQAVVVGIVGIVMIAYVLLGGMKGTTYVQ 199
           GT+ V L Y++ QMAGAG+L+ ++L +       V V +VGI MI YVL GGM  TT+VQ
Sbjct: 123 GTVVVNLAYMVPQMAGAGALIKLMLGVP----YDVAVVLVGIGMIVYVLFGGMIATTWVQ 178

Query: 200 MIKAVLLVGGVAIMTVLTFVKVSGGLTTLLNDAVEKHAASDYAATKGYDPTQILEPGLQY 259
           ++KA+LL+    ++  +    V      L   +VE+   S   A+ GY            
Sbjct: 179 IVKAMLLLVAACVLVSMLLAAVRFNPLALFA-SVERLYGSKMLASGGY------------ 225

Query: 260 GATLTTQLDFISLALALCLGTAGLPHVLMRFYTVPTAKEARKSVTWAIVLIGAFYLMTLV 319
                  LD +SL ++   G AGLPH++ RFYTVP A+ ARKSV W + L G+F+++T +
Sbjct: 226 ---FHHPLDTMSLFISFIFGVAGLPHIMTRFYTVPDARTARKSVLWLMFLAGSFFMVTTL 282

Query: 320 LGYGAAALVGPDRVIAAPGAANAAAPLLAF-------ELGGSIFMALISAVAFATVLAVV 372
           +G+ +A  VG D + AA    N A PLLA         LGG IF+A I A+AFA +LAVV
Sbjct: 283 IGFASAVFVGQDAIRAADKGGNLALPLLAQYLGGGAGSLGGQIFLASICAIAFAAILAVV 342

Query: 373 AGLAITASAAVGHDIYNAVIRNGQSTEAEQVRVSRITVVVIGLISIVLGILAMTQNVAFL 432
           AGL + +S A+ HD+Y  V+R G  ++AEQVRV+RI  V +G+ +I L +LA   NV  L
Sbjct: 343 AGLTLASSGAIAHDLYVNVLRKGAVSDAEQVRVARIATVAVGIAAIGLSLLAQGLNVGVL 402

Query: 433 VALAFAVAASANLPTILYSLYWKKFNTTGAVAAIYTGLISALLLIFLSPAVSGNDSAMVP 492
           V LA +VAAS+N P IL S++W++FNT G +  +  GL S++ L F+ PA  G+      
Sbjct: 403 VILAISVAASSNFPIILLSIFWRRFNTAGVIGGVIGGLTSSVALAFVGPAFMGSH----- 457

Query: 493 GADWAIFPLKNPGLVSIPLAFIAGWIGTLVGKPDNMDDLAAE-MEVRSLTGV 543
               A+FP+ NP +VS+P+   + W+ T++ +P    D   E   +R+ TG+
Sbjct: 458 ----ALFPIVNPAIVSLPIGLFSAWLCTMLSRPTPTQDGDFEAFYLRAQTGI 505


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: 623
Number of extensions: 31
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: 551
Length of database: 516
Length adjustment: 35
Effective length of query: 516
Effective length of database: 481
Effective search space:   248196
Effective search space used:   248196
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 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