GapMind for catabolism of small carbon sources

 

Alignments for a candidate for permease in Cupriavidus basilensis 4G11

Align histidine permease (characterized)
to candidate RR42_RS14635 RR42_RS14635 proline-specific permease

Query= reanno::pseudo3_N2E3:AO353_12275
         (468 letters)



>FitnessBrowser__Cup4G11:RR42_RS14635
          Length = 466

 Score =  709 bits (1831), Expect = 0.0
 Identities = 349/458 (76%), Positives = 404/458 (88%), Gaps = 1/458 (0%)

Query: 1   MQKPANGLKRGLSARHIRFMALGSAIGTGLFYGSASAIQMAGPAVLLAYLIGGAAVFMVM 60
           MQ+ + GL+RGLSARHIRFMALGSAIGTGLFYGSASAIQ AGPAVLLAY+IGGAAV+MVM
Sbjct: 1   MQEQSQGLQRGLSARHIRFMALGSAIGTGLFYGSASAIQTAGPAVLLAYVIGGAAVYMVM 60

Query: 61  RALGEMAVHNPVAGSFGQYASTYLGPMAGFILGWTYAFEMVIVGMADVTAFGIYMGFWFP 120
           RALGEMAV NPVAGSFGQYAST LGP+AGF+LGWTYAFEM++V +ADVTAFGIYMGFWFP
Sbjct: 61  RALGEMAVRNPVAGSFGQYASTGLGPLAGFLLGWTYAFEMIVVCLADVTAFGIYMGFWFP 120

Query: 121 EVSRWIWVLGVVSIVGGLNLCNVKVFGEMEFWLSLLKVAAIVAMILGGFGIMLFGISTAP 180
           +V RWIWVLG+V ++GGLNL +VKVFGE+EFWLSLLKV AIVAMI GG  IMLFG   A 
Sbjct: 121 DVPRWIWVLGIVFLIGGLNLLSVKVFGELEFWLSLLKVGAIVAMIGGGVAIMLFGFGMAD 180

Query: 181 GQV-TDISNLWTQGGFMPNGMGGLIASFAVVMFAFGGIEIIGVTAGEAKDPQHVLPRAIN 239
           G V T I NLWT GGFMPNG+ G+IASFAVVMFAFGGIEIIG+TAGEA+DPQ V+PRAIN
Sbjct: 181 GGVATGIHNLWTHGGFMPNGIAGVIASFAVVMFAFGGIEIIGITAGEARDPQRVIPRAIN 240

Query: 240 AVPLRILLFYVLTMLVLMSIFPWQQIGSQGSPFVQIFDKLGISSAATILNIVVITAAISA 299
           AVPLRILLFYVLT+ VLMS++PW +IGS+GSPFVQIF +LGI SAA +LNIVVI+AA+SA
Sbjct: 241 AVPLRILLFYVLTLAVLMSLYPWHRIGSEGSPFVQIFSRLGIGSAAAVLNIVVISAAVSA 300

Query: 300 INSDIFGAGRMMFGLAQQGHAPKGFAHLSRNGVPWMTVVVMSVALLLGVLLNYLIPENVF 359
           INSDIFGAGRM++G+A Q  AP+ FA +SR GVPWMTVVVM+ ALL GV+LNY++PE+VF
Sbjct: 301 INSDIFGAGRMLYGMAVQRQAPRIFASVSRKGVPWMTVVVMAFALLAGVVLNYVMPEDVF 360

Query: 360 LLIASIATFATVWVWLMILFTQVAMRRSMTAEQVAQLKFPVPFWPYAPMAAIAFMLFVFG 419
            LIASIATFATVWVWLMIL +QVA+RR M+  +VA LKFPVPFWP AP+AA AFMLF+FG
Sbjct: 361 TLIASIATFATVWVWLMILLSQVALRRRMSRAEVAALKFPVPFWPVAPLAATAFMLFIFG 420

Query: 420 VLGYFPDTQAALIVGVVWIVLLVLAYLMWVKPAAGQAA 457
           VLG+FP T+AAL+VG VW++LLV+A+  W +P   + A
Sbjct: 421 VLGWFPQTRAALLVGAVWLLLLVVAWWCWGRPRGQEGA 458


Lambda     K      H
   0.329    0.142    0.441 

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: 895
Number of extensions: 54
Number of successful extensions: 2
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: 468
Length of database: 466
Length adjustment: 33
Effective length of query: 435
Effective length of database: 433
Effective search space:   188355
Effective search space used:   188355
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 (21.8 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:

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