Alignments for a candidate for mctP in Azorhizobium caulinodans ORS 571

GapMind for catabolism of small carbon sources

Alignments for a candidate for mctP in Azorhizobium caulinodans ORS 571

Align Monocarboxylate transport permease protein (characterized)
to candidate WP_012169553.1 AZC_RS05235 sodium:solute symporter family protein

Query= SwissProt::Q1M7A2
         (491 letters)



>NCBI__GCF_000010525.1:WP_012169553.1
          Length = 494

 Score =  707 bits (1824), Expect = 0.0
 Identities = 349/482 (72%), Positives = 405/482 (84%), Gaps = 1/482 (0%)

Query: 10  LAVFIFFFVLVTVMGFVASRWRKPETLAHIDEWGLGGRNFGTWITWFLVGGDFYTAYTVI 69
           L+VF+ FF LVT+MGFVASRW+K +  A +DEWGLGGR FG WITWFLVGGDFYTAYTVI
Sbjct: 10  LSVFLVFFALVTIMGFVASRWKKADNHAKLDEWGLGGRQFGVWITWFLVGGDFYTAYTVI 69

Query: 70  AVPALVYTVGAYGFFALPYTIVVYPFVFMVMPVLWKRAKDFGYVTAGDVVHGQYGSRGLE 129
           AVPALVY VGAYGFFALPYTIVVYPF+F+VMP LWK A   G+VTA DVVHG Y +R LE
Sbjct: 70  AVPALVYAVGAYGFFALPYTIVVYPFIFLVMPRLWKVAHAAGHVTAADVVHGTYNNRWLE 129

Query: 130 LAVAATGVIATMPYIALQLVGMTAVLKALGLHGELPLAIAFIVLALYTYSAGLRAPALIA 189
           LAVA TG++ATMPYIALQLVGM AV+ A+GL GELP+ +AF++LALYTYSAGLRAPALIA
Sbjct: 130 LAVALTGLVATMPYIALQLVGMQAVIGAMGLKGELPIIVAFLILALYTYSAGLRAPALIA 189

Query: 190 FVKDIMIYIVVIAAVALIPSKLGGYANVFASADAAFQAKGSGN-LLLGGNQYVAYATLAL 248
           FVKD+MIYIVVI AV ++P  LGGY  VF++ADA + AKG    L+L   Q + YATLAL
Sbjct: 190 FVKDVMIYIVVIVAVVVVPMHLGGYGAVFSAADAVYAAKGGNTGLVLKDAQMLPYATLAL 249

Query: 249 GSALAAFMYPHTLTGIFASNSGKTIRKNAIMLPAYTLLLGLLALLGYMGHAANLKLDSAN 308
           GSALAAFMYPHTLTGIFA+ S  TIR NA++LPAYT+LLGL+ALLGYM HAA +K+ S  
Sbjct: 250 GSALAAFMYPHTLTGIFAAKSANTIRSNAVLLPAYTVLLGLIALLGYMAHAAGVKVTSPT 309

Query: 309 DVVPTLFKTLFSGWFSGFAFAAIAIGALVPAAVMSIGAANLFTRNFWKAYVDPDVSDAGE 368
           DVVP LF+TLFSGWFSGFAFAAI IGALVPAAVMSIGA+NLFTRN WKAYV+P V++AGE
Sbjct: 310 DVVPVLFQTLFSGWFSGFAFAAIGIGALVPAAVMSIGASNLFTRNVWKAYVNPQVTEAGE 369

Query: 369 AKVAKITSLVVKVGALLVIIFLPTQFALDLQLLGGIWILQTLPALVFGLYTNWFRAPGLL 428
           A+VAKI SLVVKVGAL  I+F+PT+FA+DLQLLGG+WILQT P+LVFGL+T WFRAP LL
Sbjct: 370 AQVAKIVSLVVKVGALACIVFMPTKFAIDLQLLGGLWILQTFPSLVFGLFTRWFRAPALL 429

Query: 429 AGWFVGFGGGTFLVWDAGWKPLHLISLGGEPFTVYTGLLALAANIAVAVVVNALLPAKAP 488
           AGW VG  GGT + +  G  P+H + +GG+ +T+Y GLLA AAN+ VAVVVNALL A +P
Sbjct: 430 AGWLVGIVGGTTVAFADGLVPVHTLVIGGQNYTIYVGLLAFAANVIVAVVVNALLAATSP 489

Query: 489 VR 490
            R
Sbjct: 490 KR 491


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: 912
Number of extensions: 61
Number of successful extensions: 3
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: 494
Length adjustment: 34
Effective length of query: 457
Effective length of database: 460
Effective search space:   210220
Effective search space used:   210220
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 Apr 09 2024. The underlying query database was built on Sep 17 2021.

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Protein sequences (fasta format)
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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