GapMind for catabolism of small carbon sources

 

Aligments for a candidate for alsT in Klebsiella michiganensis M5al

Align Amino-acid carrier protein, AlsT (characterized)
to candidate BWI76_RS04265 BWI76_RS04265 sodium:alanine symporter family protein

Query= TCDB::Q45068
         (465 letters)



>lcl|FitnessBrowser__Koxy:BWI76_RS04265 BWI76_RS04265 sodium:alanine
           symporter family protein
          Length = 476

 Score =  381 bits (979), Expect = e-110
 Identities = 208/478 (43%), Positives = 298/478 (62%), Gaps = 23/478 (4%)

Query: 5   FNSLINIPSDFIW-KYLFYILIGLGLFFTIRFGFIQFRYFIEMFRIVGEKPEGNKG-VSS 62
           F S IN   + +W   + Y+L+G G++FT R  FIQFRY  +  + +    +   G ++S
Sbjct: 4   FLSFIN---EILWGSVMIYLLLGAGVWFTWRTKFIQFRYIRQFSKSLKRSLQPQPGGLTS 60

Query: 63  MQAFFISAASRVGTGNLTGVALAIATGGPGAVFWMWVVAAVGMASSFVESTLAQLYKVRD 122
            QA  +S A+RVG+GN+ GVALAIA GGPGAVFWMW+ A +GMASSF E +LAQLYK RD
Sbjct: 61  FQALCMSLAARVGSGNMAGVALAIAAGGPGAVFWMWLSALLGMASSFAECSLAQLYKERD 120

Query: 123 GE-DFRGGPAYYIQKGLGARWLGIVFAILITVSFGLIFNAVQTNTIAGALDGAFHVNKIV 181
               FRGGPA+Y+ +GLG RW+G++F+I + +++G+IFN VQ N++A A+  AFH+ + +
Sbjct: 121 SRGQFRGGPAWYMARGLGMRWMGVLFSIFLLLAYGIIFNTVQANSVAHAMAYAFHLPEAI 180

Query: 182 VAIVLAVLTAFIIFGGLKRVVAVSQLIVPVMAGIYILIALFVVITNITAFPGVIATIVKN 241
              VLAVLT  +I  G++ V  + Q +VPVMA +++  +L + + +ITA P +  TI + 
Sbjct: 181 TGGVLAVLTLLVIVRGIRGVARMMQWLVPVMALLWVATSLVIGLWHITALPTIFETIFRC 240

Query: 242 ALGFEQVVGGGIGGII----VIGAQRGLFSNEAGMGSAPN--AAATAHVSHPAKQGFIQT 295
           A G+++   G +G  I      G QRG+FSNEAGMGS PN  AAA +   HPA QG +Q 
Sbjct: 241 AFGWQEAAAGAVGYTISQALTSGFQRGMFSNEAGMGSTPNSAAAAASWPPHPAAQGIVQM 300

Query: 296 LGVFFDTFIICTSTAFIILLYSVTPKGD---GIQVTQAALNHHIGGWAPTFIAVAMFLFA 352
           +GVF DT +ICT++A II+L      G+   GIQ  Q ++N+ IG W  +F+A+ + LFA
Sbjct: 301 IGVFIDTIVICTASAVIIMLAPRDGNGEAVNGIQAIQHSMNNLIGDWGSSFVAIVVLLFA 360

Query: 353 FSSVVGNYYYGETNIEFIKTS---KTWLNIYRIAVIAMVVYGSLSGFQIVWDMADLFMGI 409
           FSS+V NY Y E N+ F++       WL   R+  + MV  G++ G  +VW MAD  M +
Sbjct: 361 FSSIVANYIYAENNLIFLRMDSDRNIWL--LRLLTLCMVATGAMIGLPVVWQMADTIMAL 418

Query: 410 MALINLIVIALLSNVAYKVYKDYAKQRKQGLDPVFKAKNIPGLKN---AETWEDEKQE 464
           MA+ NL  I LLS     +  DY +QR+ G  P F     P +       TW++  +E
Sbjct: 419 MAITNLTAILLLSPTVRIIASDYLRQRRLGQRPEFDVTRYPEIHQQLVPGTWDNLPRE 476


Lambda     K      H
   0.327    0.142    0.426 

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: 553
Number of extensions: 18
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: 465
Length of database: 476
Length adjustment: 33
Effective length of query: 432
Effective length of database: 443
Effective search space:   191376
Effective search space used:   191376
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: 51 (24.3 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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