Alignments for a candidate for mctP in Streptacidiphilus oryzae TH49

GapMind for catabolism of small carbon sources

Alignments for a candidate for mctP in Streptacidiphilus oryzae TH49

Align Monocarboxylate transport permease protein (characterized)
to candidate WP_037573002.1 BS73_RS15850 sodium:solute symporter

Query= SwissProt::Q1M7A2
         (491 letters)



>NCBI__GCF_000744815.1:WP_037573002.1
          Length = 543

 Score =  533 bits (1372), Expect = e-156
 Identities = 286/512 (55%), Positives = 353/512 (68%), Gaps = 24/512 (4%)

Query: 1   MTTDINGTALAVFIFFFVLVTVMGFVASRWRKPETLAHIDEWGLGGRNFGTWITWFLVGG 60
           M   +NG AL VFIFFF LVTV+GF+A+RWR+ +   H+DEWGLGGR+FGTWITWFL+GG
Sbjct: 1   MNHGLNGVALGVFIFFFALVTVLGFLAARWRRADNALHLDEWGLGGRSFGTWITWFLLGG 60

Query: 61  DFYTAYTVIAVPALVYTVGAYGFFALPYTIVVYPFVFMVMPVLWKRAKDFGYVTAGDVVH 120
           D YTAYT IAVPA V+  G  GFFA+PYTI+ YP VF+ +P LW  +   GYVT  D V 
Sbjct: 61  DLYTAYTFIAVPAAVFGTGGAGFFAVPYTIICYPLVFLFLPRLWSVSHRRGYVTPADFVK 120

Query: 121 GQYGSRGLELAVAATGVIATMPYIALQLVGMTAVLKALGLHG------ELPLAIAFIVLA 174
           G+YGSRGL LAVA TG++ATMPYIALQLVG+ AVL  LGL G      +LPL IAF VLA
Sbjct: 121 GRYGSRGLSLAVALTGILATMPYIALQLVGIQAVLDTLGLGGSSGFMKDLPLLIAFAVLA 180

Query: 175 LYTYSAGLRAPALIAFVKDIMIYIVVIAAVALIPSKLGGYANVFASADAAFQ------AK 228
            YTYS+GLRAPALIAFVKD +IYIV+I A   IP +LGG+ +VF SA  +         K
Sbjct: 181 AYTYSSGLRAPALIAFVKDTLIYIVIIVAAIYIPMRLGGWGHVFHSAADSLSKTNPATGK 240

Query: 229 GSGNLLLGGNQYVAYATLALGSALAAFMYPHTLTGIFASNSGKTIRKNAIMLPAYTLLLG 288
             G+L++G     AYATLALGSA+A FMYPH++TG+ +S S  T+R+N  +LPAY+L+LG
Sbjct: 241 PKGSLIVGAQGQWAYATLALGSAMALFMYPHSVTGVLSSKSRVTVRRNTAVLPAYSLMLG 300

Query: 289 LLALLGYMGHAANLKLD----SANDVVPTLFKTLFSGWFSGFAFAAIAIGALVPAAVMSI 344
            LALLG+M  AA +       +A   VP LF  +F  WF+G AFAAI IGALVPAA+MSI
Sbjct: 301 FLALLGFMAIAAGVGKGVTGFNAQLAVPELFDRMFPSWFTGIAFAAIGIGALVPAAIMSI 360

Query: 345 GAANLFTRNFWKAYVDPDVSDAGEAKVAKITSLVVKVGALLVIIFLPTQFALDLQLLGGI 404
            AANLFTRN ++ ++ PD +   E KV+KI SL+VKVGAL+ ++ +   FA++LQLLGGI
Sbjct: 361 AAANLFTRNVFRDFIKPDATPEQETKVSKIVSLLVKVGALVFVLGMDKSFAINLQLLGGI 420

Query: 405 WILQTLPALVFGLYTNWFRAPGLLAGWFVGFGGGTFLVWD--AGWKP-LHL----ISLGG 457
           WILQT P+LV GL+T WF    LL GW  G   GT+  +   A  KP  H     +++ G
Sbjct: 421 WILQTFPSLVGGLFTRWFHRWALLIGWAAGMAYGTWGAYSVAAPGKPGSHFGGSSVNIPG 480

Query: 458 EPFTVYTGLLALAANIAVAVVVNALLPA-KAP 488
              T Y GL A   N  VAVV   +  A KAP
Sbjct: 481 LGHTGYVGLTAFVLNAVVAVVFTLIFRALKAP 512


Lambda     K      H
   0.327    0.142    0.439 

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: 884
Number of extensions: 51
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: 491
Length of database: 543
Length adjustment: 35
Effective length of query: 456
Effective length of database: 508
Effective search space:   231648
Effective search space used:   231648
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 (21.7 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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Steps (tab-delimited)
Rules (tab-delimited)
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 2024 update on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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