Alignments for a candidate for CAT1 in Methylocella silvestris BL2

GapMind for catabolism of small carbon sources

Alignments for a candidate for CAT1 in Methylocella silvestris BL2

Align high affinity cationic amino acid transporter 1 (characterized)
to candidate WP_012589784.1 MSIL_RS03830 amino acid permease

Query= CharProtDB::CH_091324
         (622 letters)



>NCBI__GCF_000021745.1:WP_012589784.1
          Length = 494

 Score =  272 bits (695), Expect = 3e-77
 Identities = 161/417 (38%), Positives = 233/417 (55%), Gaps = 20/417 (4%)

Query: 24  EESRLSRCLNTYDLVALGVGSTLGAGVYVLAGAVARENAGPAIVISFLIAALASVLAGLC 83
           E   L R L+   L++LG+G  +GAG++VL G  A   AGPAI +SF++A L   LAGLC
Sbjct: 25  ETPNLRRTLSLASLISLGIGCIIGAGIFVLTGHAAAAYAGPAISLSFVLAGLVCALAGLC 84

Query: 84  YGEFGARVPKTGSAYLYSYVTVGELWAFITGWNLILSYIIGTSSVARAWSATF-----DE 138
           Y E  + VP  GSAY Y+Y T+GE  A+I GW+L+L Y  G ++VA  WS        D 
Sbjct: 85  YAEMASTVPVAGSAYTYAYATLGEFIAWIIGWDLLLEYAFGATTVAIGWSGYVVSFLRDF 144

Query: 139 LIGKPIG------EFSRQHMALNAPGVLAQTPDIFAVIIIIILTGLLTLGVKESAMVNKI 192
            IG P         F     A    G L   P   AV I++ LT LL +GV ESA VN I
Sbjct: 145 HIGIPAALAGAPFAFDPASGAWTHTGALVNAP---AVAIVLALTALLVVGVNESAKVNNI 201

Query: 193 FTCINVLVLCFIVVSGFVKGSIKNWQLTEKNFSCNNNDTNVKYGEGGFMPFGFSGVLSGA 252
              I + ++   +++G    S  NW +T  N        N   GE     +G+SG+L GA
Sbjct: 202 IVAIKLAIIVVFILAGLSSVSTANW-VTSANPDGAFIPPNAGPGE-----YGWSGILRGA 255

Query: 253 ATCFYAFVGFDCIATTGEEVKNPQKAIPVGIVASLLICFIAYFGVSAALTLMMPYFCLDI 312
           A  F+A++GFD ++T  +E KNPQ+ +P+GI+ SL+IC + Y  VS  +T ++P+  L +
Sbjct: 256 AVVFFAYIGFDAVSTAAQEAKNPQRDMPLGILGSLVICTVLYVLVSIVITGIVPFDRLSV 315

Query: 313 DSPLPGAFKHQGWEEAKYAVAIGSLCALSTSLLGSMFPMPRVIYAMAEDGLLFKFLAKIN 372
             P+       G       V +G++  LS+ +L  +    RV+Y++A DGLL    AK++
Sbjct: 316 PDPIALGVDVIGLRWLSTVVKLGAILGLSSVVLVLLLGQTRVLYSIARDGLLPPIAAKVH 375

Query: 373 NRTKTPVIATVTSGAIAAVMAFLFELKDLVDLMSIGTLLAYSLVAACVLVLRYQPEQ 429
            R +TP + T+ +G I AVMA +  +  + +L+SIGTL A+++V A VL LRY   Q
Sbjct: 376 PRFRTPYLTTIGTGLIVAVMAGVLPIGLVGELVSIGTLFAFAIVCAGVLFLRYTHPQ 432



 Score = 64.3 bits (155), Expect = 1e-14
 Identities = 38/129 (29%), Positives = 63/129 (48%), Gaps = 9/129 (6%)

Query: 479 VEPSKFSGLIVNISAGLLAALIITVCIVAVLGREALAEGTLWAVFVMTGSVLLCMLVTGI 538
           V P   +  +  I  GL+ A++  V  + ++G E ++ GTL+A  ++   VL        
Sbjct: 374 VHPRFRTPYLTTIGTGLIVAVMAGVLPIGLVG-ELVSIGTLFAFAIVCAGVLFL------ 426

Query: 539 IWRQPESKTKLSFKVPFVPVLPVLSIFVNIYLMMQLDQGTWVRFAVWMLIGFTIYFGYGI 598
             R    +    F+ P + ++  L     + LM+ L + TW+RFA+W+ IG  +YF YG 
Sbjct: 427 --RYTHPQIHRPFRAPLIAIVAPLGAAAAVVLMLGLPRDTWIRFAIWLAIGLILYFTYGR 484

Query: 599 WHSEEASLA 607
            HS  A  A
Sbjct: 485 RHSRLARAA 493


Lambda     K      H
   0.324    0.138    0.417 

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: 795
Number of extensions: 39
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 622
Length of database: 494
Length adjustment: 36
Effective length of query: 586
Effective length of database: 458
Effective search space:   268388
Effective search space used:   268388
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 (21.6 bits)
S2: 53 (25.0 bits)

This GapMind analysis is from Apr 09 2024. 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:

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