GapMind for catabolism of small carbon sources

 

Alignments for a candidate for actP in Methanospirillum lacunae Ki8-1

Align Monocarboxylic acid transporter (characterized)
to candidate WP_109969114.1 DK846_RS11580 cation acetate symporter

Query= SwissProt::Q8NS49
         (551 letters)



>NCBI__GCF_003173355.1:WP_109969114.1
          Length = 502

 Score =  400 bits (1028), Expect = e-116
 Identities = 218/504 (43%), Positives = 315/504 (62%), Gaps = 23/504 (4%)

Query: 21  LNISVFVVFIIVTMTVVLRVGKSTSESTDFYTGGASFSGTQNGLAIAGDYLSAASFLGIV 80
           L  ++FV+  + T+ +     +    ++ FYT G       NG+A AGDYLSAASFLGI 
Sbjct: 8   LAFTIFVLITLSTLALSFYAARRVRTASHFYTAGGGVKWFVNGIAFAGDYLSAASFLGIA 67

Query: 81  GAISLNGYDGFLYSIGFFVAWLVALLLVAEPLRNVGRFTMADVLSFRLRQKPVRVAAACG 140
           G I+ +G+DGF+YSIGF   W+VALL++AEPLR +G+FT  D L++R   K +R+ AA  
Sbjct: 68  GMIAFSGFDGFMYSIGFLAGWIVALLIIAEPLRKIGKFTFGDALAWRFASKKIRLCAALS 127

Query: 141 TLAVTLFYLIAQMAGAGSLVSVLLDIHEFKWQAVVVGIVGIVMIAYVLLGGMKGTTYVQM 200
            L V++FYLI QM GAGS++  L+ +    ++A V+ IVG V+I  V   GM  TTYVQ 
Sbjct: 128 ALVVSIFYLIPQMVGAGSIIQPLIGL---PYEAGVI-IVGAVVILIVATAGMVSTTYVQF 183

Query: 201 IKAVLLVGGVAIMTVLTFVKVSGGLTTLLNDAVEKHAASDYAATKGYDPTQILEPGLQYG 260
           IK  LL+     +TV        G    ++  +   A +  A+         + PG+++ 
Sbjct: 184 IKGFLLLIAAGALTVGVLAVAGMGPLEFISTVLNSPAITVPASNGTVTGDVFMTPGMKF- 242

Query: 261 ATLTTQLDFISLALALCLGTAGLPHVLMRFYTVPTAKEARKSVTWAIVLIGAFYLMTLVL 320
                 LDF SLAL L LGTA LPH+L+R++TVPT  +ARKS   AI+ IG FY++TL L
Sbjct: 243 ---KNPLDFASLALGLILGTAALPHILIRYFTVPTPADARKSTVVAIIAIGVFYVLTLFL 299

Query: 321 GYGAAALVGPDRVIAAPGAANAAAPLLAFELGGSIFMALISAVAFATVLAVVAGLAITAS 380
           G GA   +  D     P  +N +APLLA  +GG  F A+I+++AFAT+L  V+GL I A+
Sbjct: 300 GLGANYFMTVD-----PKNSNLSAPLLAEFIGGEWFFAIIASIAFATILGTVSGLIIAAA 354

Query: 381 AAVGHDIYNAVIRNGQSTEAEQVRVSRITVVVIGLISIVLGILAMTQNVAFLVALAFAVA 440
            A+ HDIY  V+   +S + + +R+S++T V +G+I+I+LGI++  QNVAFLV LAFA+A
Sbjct: 355 GAIAHDIYTEVM-GRRSDDKKALRISKLTAVTVGVIAIILGIISKGQNVAFLVGLAFAIA 413

Query: 441 ASANLPTILYSLYWKKFNTTGAVAAIYTGLISALLLIFLSPAVSGNDSAMVPGADWAIFP 500
           ASAN+P ++ +L+WK+    G +A I TGL+ ++ LI +SP V G           A+FP
Sbjct: 414 ASANIPALICTLFWKRSTERGIIAGILTGLLLSVSLILISPTVMGKA---------ALFP 464

Query: 501 LKNPGLVSIPLAFIAGWIGTLVGK 524
           L+NPG++SIPL F+   + +L GK
Sbjct: 465 LENPGIISIPLGFLVTILVSLTGK 488


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: 626
Number of extensions: 25
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: 551
Length of database: 502
Length adjustment: 35
Effective length of query: 516
Effective length of database: 467
Effective search space:   240972
Effective search space used:   240972
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